Merge branch 'master' into staging.

With "conflicts" solved (all in favor of master except git) in:
	gnu/local.mk
	gnu/packages/databases.scm
	gnu/packages/glib.scm
	gnu/packages/gnome.scm
	gnu/packages/gnupg.scm
	gnu/packages/gnuzilla.scm
	gnu/packages/graphics.scm
	gnu/packages/gstreamer.scm
	gnu/packages/gtk.scm
	gnu/packages/linux.scm
	gnu/packages/machine-learning.scm
	gnu/packages/networking.scm
	gnu/packages/polkit.scm
	gnu/packages/pulseaudio.scm
	gnu/packages/rpc.scm
	gnu/packages/rust.scm
	gnu/packages/version-control.scm
	gnu/packages/w3m.scm

1 files changed, 4966 insertions, 4475 deletions

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4cbffac000..534204a16a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,16 +1,17 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
+;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -72,7 +73,7 @@
      `((upstream-name . "org.EcK12.eg.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
     (synopsis "Genome wide annotation for E coli strain K12")
     (description
@@ -102,7 +103,7 @@ analysis.")
     (properties `((upstream-name . "org.Bt.eg.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://bioconductor.org/packages/org.Bt.eg.db")
     (synopsis "Genome wide annotation for Bovine")
     (description
@@ -124,7 +125,7 @@ based on mapping using Entrez Gene identifiers.")
     (properties `((upstream-name . "reactome.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://bioconductor.org/packages/reactome.db/")
     (synopsis "Annotation maps for reactome")
     (description
@@ -147,7 +148,7 @@ database, assembled using data from REACTOME.")
      `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)))
+     (list r-bsgenome))
     (home-page
      "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
     (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
@@ -170,7 +171,7 @@ taurus (UCSC version bosTau8).")
      `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)))
+     (list r-bsgenome))
     (home-page
      "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
     (synopsis "Full genome sequences for Worm")
@@ -195,7 +196,7 @@ objects.")
      `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)))
+     (list r-bsgenome))
     (home-page
      "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
     (synopsis "Full genome sequences for Worm")
@@ -220,7 +221,7 @@ objects.")
      `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)))
+     (list r-bsgenome))
     (home-page
      "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
     (synopsis "Full genome sequences for Fly")
@@ -245,7 +246,7 @@ objects.")
      `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)))
+     (list r-bsgenome))
     (home-page
      "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
     (synopsis "Full genome sequences for Fly")
@@ -270,9 +271,7 @@ Biostrings objects.")
      `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-dmelanogaster-ucsc-dm3"
-        ,r-bsgenome-dmelanogaster-ucsc-dm3)))
+     (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3))
     (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
     (synopsis "Full masked genome sequences for Fly")
     (description
@@ -286,6 +285,28 @@ RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
 Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-drerio-ucsc-danrer11
+  (package
+    (name "r-bsgenome-drerio-ucsc-danrer11")
+    (version "1.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer11"
+                              version 'annotation))
+       (sha256
+        (base32 "08a928mqzv2jxngjcs4yr6ni1b9z9al6jdngwi438j8hm41cwk4v"))))
+    (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-bsgenome))
+    (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11")
+    (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)")
+    (description
+     "This package provides full genome sequences for Danio rerio (Zebrafish)
+as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
   (package
     (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
@@ -301,7 +322,7 @@ Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
      `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)))
+     (list r-bsgenome))
     (home-page
      "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
     (synopsis "Full genome sequences for Homo sapiens")
@@ -324,7 +345,7 @@ Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
          "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
     (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
+    (propagated-inputs (list r-bsgenome))
     (home-page
      "https://bioconductor.org/packages/release/data/annotation/html/\
 BSgenome.Hsapiens.NCBI.GRCh38.html")
@@ -349,9 +370,7 @@ provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-hsapiens-ucsc-hg19"
-        ,r-bsgenome-hsapiens-ucsc-hg19)))
+     (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19))
     (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
     (synopsis "Full masked genome sequences for Homo sapiens")
     (description
@@ -380,7 +399,7 @@ default.")
      `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)))
+     (list r-bsgenome))
     (home-page
      "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
     (synopsis "Full genome sequences for Mouse")
@@ -404,9 +423,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
      `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-mmusculus-ucsc-mm9"
-        ,r-bsgenome-mmusculus-ucsc-mm9)))
+     (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9))
     (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
     (synopsis "Full masked genome sequences for Mouse")
     (description
@@ -435,7 +452,7 @@ default."  )
      `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)))
+     (list r-bsgenome))
     (home-page
      "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
     (synopsis "Full genome sequences for Mouse")
@@ -478,7 +495,7 @@ ID and species.  It is used by functions in the GenomeInfoDb package.")
      `((upstream-name . "GO.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://bioconductor.org/packages/GO.db")
     (synopsis "Annotation maps describing the entire Gene Ontology")
     (description
@@ -500,12 +517,12 @@ information about the latest version of the Gene Ontologies.")
      `((upstream-name . "Homo.sapiens")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-go-db" ,r-go-db)
-       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
-       ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
-       ("r-organismdbi" ,r-organismdbi)
-       ("r-annotationdbi" ,r-annotationdbi)))
+     (list r-genomicfeatures
+           r-go-db
+           r-org-hs-eg-db
+           r-txdb-hsapiens-ucsc-hg19-knowngene
+           r-organismdbi
+           r-annotationdbi))
     (home-page "https://bioconductor.org/packages/Homo.sapiens/")
     (synopsis "Annotation package for the Homo.sapiens object")
     (description
@@ -527,13 +544,12 @@ several related annotation packages.")
     (properties `((upstream-name . "Mus.musculus")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-go-db" ,r-go-db)
-       ("r-org-mm-eg-db" ,r-org-mm-eg-db)
-       ("r-organismdbi" ,r-organismdbi)
-       ("r-txdb-mmusculus-ucsc-mm10-knowngene"
-        ,r-txdb-mmusculus-ucsc-mm10-knowngene)))
+     (list r-annotationdbi
+           r-genomicfeatures
+           r-go-db
+           r-org-mm-eg-db
+           r-organismdbi
+           r-txdb-mmusculus-ucsc-mm10-knowngene))
     (home-page "https://bioconductor.org/packages/Mus.musculus")
     (synopsis "Annotation package for the Mus.musculus object")
     (description
@@ -555,7 +571,7 @@ from several related annotation packages.")
      `((upstream-name . "org.Ce.eg.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
     (synopsis "Genome wide annotation for Worm")
     (description
@@ -577,7 +593,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
      `((upstream-name . "org.Dm.eg.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
     (synopsis "Genome wide annotation for Fly")
     (description
@@ -599,7 +615,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
      `((upstream-name . "org.Dr.eg.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
     (synopsis "Annotation for Zebrafish")
     (description
@@ -610,18 +626,18 @@ based on mapping using Entrez Gene identifiers.")
 (define-public r-org-hs-eg-db
   (package
     (name "r-org-hs-eg-db")
-    (version "3.7.0")
+    (version "3.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
               (sha256
                (base32
-                "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
+                "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j"))))
     (properties
      `((upstream-name . "org.Hs.eg.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
     (synopsis "Genome wide annotation for Human")
     (description
@@ -643,7 +659,7 @@ on mapping using Entrez Gene identifiers.")
      `((upstream-name . "org.Mm.eg.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
     (synopsis "Genome wide annotation for Mouse")
     (description
@@ -666,7 +682,7 @@ annotations for the genome of the model mouse Mus musculus.")
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)))
+     (list r-bsgenome))
     (home-page
      "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
     (synopsis "Full genome sequences for Homo sapiens")
@@ -690,7 +706,7 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.")
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)))
+     (list r-bsgenome))
     (home-page
      "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
     (synopsis "Full genome sequences for Homo sapiens")
@@ -714,7 +730,7 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
      `((upstream-name . "EnsDb.Hsapiens.v75")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-ensembldb" ,r-ensembldb)))
+     (list r-ensembldb))
     (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
     (synopsis "Ensembl based annotation package")
     (description
@@ -737,8 +753,7 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
      `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-genomicfeatures" ,r-genomicfeatures)))
+     (list r-annotationdbi r-genomicfeatures))
     (home-page
      "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
     (synopsis "Annotation package for TxDb object(s)")
@@ -762,7 +777,7 @@ exposing these as TxDb objects.")
      `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-genomicfeatures" ,r-genomicfeatures)))
+     (list r-genomicfeatures))
     (home-page
      "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
     (synopsis "Annotation package for human genome in TxDb format")
@@ -787,7 +802,7 @@ track.  The database is exposed as a @code{TxDb} object.")
      `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-genomicfeatures" ,r-genomicfeatures)))
+     (list r-genomicfeatures))
     (home-page
      "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
     (synopsis "Annotation package for human genome in TxDb format")
@@ -812,8 +827,7 @@ track.  The database is exposed as a @code{TxDb} object.")
      `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-annotationdbi" ,r-annotationdbi)))
+     (list r-genomicfeatures r-annotationdbi))
     (home-page
      "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
     (synopsis "Annotation package for mouse genome in TxDb format")
@@ -838,9 +852,7 @@ database is exposed as a @code{TxDb} object.")
      `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-annotationdbi" ,r-annotationdbi)))
+     (list r-bsgenome r-genomicfeatures r-annotationdbi))
     (home-page
      "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
     (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
@@ -867,8 +879,7 @@ based on the knownGene track.")
      `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-genomicfeatures" ,r-genomicfeatures)))
+     (list r-annotationdbi r-genomicfeatures))
     (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
     (synopsis "Annotation package for C elegans TxDb objects")
     (description
@@ -891,11 +902,8 @@ by exposing these as TxDb objects.")
      `((upstream-name . "FDb.InfiniumMethylation.hg19")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
-       ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
+     (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db
+           r-txdb-hsapiens-ucsc-hg19-knowngene))
     (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
     (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
     (description
@@ -919,7 +927,7 @@ annotations.")
      `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-minfi" ,r-minfi)))
+     (list r-minfi))
     (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
     (synopsis "Manifest for Illumina's EPIC methylation arrays")
     (description
@@ -940,7 +948,7 @@ annotations.")
      `((upstream-name . "DO.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://www.bioconductor.org/packages/DO.db/")
     (synopsis "Annotation maps describing the entire Disease Ontology")
     (description
@@ -948,6 +956,26 @@ annotations.")
 Disease Ontology.")
     (license license:artistic2.0)))
 
+(define-public r-hgu133plus2-db
+  (package
+    (name "r-hgu133plus2-db")
+    (version "3.13.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "hgu133plus2.db" version 'annotation))
+       (sha256
+        (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx"))))
+    (properties `((upstream-name . "hgu133plus2.db")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
+    (home-page "https://bioconductor.org/packages/hgu133plus2.db")
+    (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data")
+    (description
+     "This package provides Affymetrix HG-U133_Plus_2 array annotation
+data (chip hgu133plus2) assembled using data from public repositories.")
+    (license license:artistic2.0)))
+
 (define-public r-pfam-db
   (package
     (name "r-pfam-db")
@@ -962,7 +990,7 @@ Disease Ontology.")
     (properties `((upstream-name . "PFAM.db")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://bioconductor.org/packages/PFAM.db")
     (synopsis "Set of protein ID mappings for PFAM")
     (description
@@ -986,12 +1014,12 @@ using data from public repositories.")
      `((upstream-name . "phastCons100way.UCSC.hg19")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-genomicscores" ,r-genomicscores)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-bsgenome
+           r-genomeinfodb
+           r-genomicranges
+           r-genomicscores
+           r-iranges
+           r-s4vectors))
     (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
     (synopsis "UCSC phastCons conservation scores for hg19")
     (description
@@ -1017,7 +1045,7 @@ species.")
      `((upstream-name . "ABAData")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
+     (list r-annotationdbi))
     (home-page "https://www.bioconductor.org/packages/ABAData/")
     (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
     (description
@@ -1055,38 +1083,38 @@ All datasets are restricted to protein coding genes.")
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AneuFinder" version))
               (sha256
                (base32
-                "0m6wphlriq7y21ih1p2kzml5jzcic79jc52kkk59dkjj8j88yllk"))))
+                "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0"))))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (propagated-inputs
-     `(("r-genomicranges" ,r-genomicranges)
-       ("r-aneufinderdata" ,r-aneufinderdata)
-       ("r-ecp" ,r-ecp)
-       ("r-foreach" ,r-foreach)
-       ("r-doparallel" ,r-doparallel)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-bamsignals" ,r-bamsignals)
-       ("r-dnacopy" ,r-dnacopy)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-reshape2" ,r-reshape2)
-       ("r-ggdendro" ,r-ggdendro)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-reordercluster" ,r-reordercluster)
-       ("r-mclust" ,r-mclust)
-       ("r-cowplot" ,r-cowplot)))
+     (list r-genomicranges
+           r-aneufinderdata
+           r-ecp
+           r-foreach
+           r-doparallel
+           r-biocgenerics
+           r-s4vectors
+           r-genomeinfodb
+           r-iranges
+           r-rsamtools
+           r-bamsignals
+           r-dnacopy
+           r-biostrings
+           r-genomicalignments
+           r-ggplot2
+           r-reshape2
+           r-ggdendro
+           r-ggrepel
+           r-reordercluster
+           r-mclust
+           r-cowplot))
     (home-page "https://bioconductor.org/packages/AneuFinder/")
     (synopsis "Copy number variation analysis in single-cell-sequencing data")
     (description "This package implements functions for copy number variant
@@ -1129,10 +1157,8 @@ from Illumina 450k methylation arrays.")
      `((upstream-name . "biscuiteerData")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationhub" ,r-annotationhub)
-       ("r-curl" ,r-curl)
-       ("r-experimenthub" ,r-experimenthub)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-annotationhub r-curl r-experimenthub))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/biscuiteerData")
     (synopsis "Data package for Biscuiteer")
     (description
@@ -1140,6 +1166,35 @@ from Illumina 450k methylation arrays.")
 biscuiteer.")
     (license license:gpl3)))
 
+(define-public r-celldex
+  (package
+    (name "r-celldex")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "celldex" version 'experiment))
+       (sha256
+        (base32 "04w60fx3s3wlirmr65nsz6d7ig48j9fzimdr8kbdqv1g80ivdcq1"))))
+    (properties `((upstream-name . "celldex")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-annotationdbi
+           r-annotationhub
+           r-delayedarray
+           r-delayedmatrixstats
+           r-experimenthub
+           r-s4vectors
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/LTLA/celldex")
+    (synopsis "Reference index for cell types")
+    (description
+     "This package provides a collection of reference expression datasets with
+curated cell type labels, for use in procedures like automated annotation of
+single-cell data or deconvolution of bulk RNA-seq.")
+    (license license:gpl3)))
+
 (define-public r-chromstardata
   (package
     (name "r-chromstardata")
@@ -1160,6 +1215,34 @@ biscuiteer.")
 chromstaR package.")
     (license license:gpl3)))
 
+(define-public r-chromvarmotifs
+  (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076")
+        (revision "1"))
+    (package
+      (name "r-chromvarmotifs")
+      (version (git-version "0.2.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/GreenleafLab/chromVARmotifs")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q"))))
+      (properties `((upstream-name . "chromVARmotifs")))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-tfbstools" ,r-tfbstools)))
+      (home-page "https://github.com/GreenleafLab/chromVARmotifs")
+      (synopsis "Stores motif collections for use with motifmatchr or chromVAR")
+      (description
+       "This package stores motif collections as lists of @dfn{position
+frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools}
+package for use in R with packages like @code{motifmatchr} or
+@code{chromVAR}.")
+      (license license:expat))))
+
 (define-public r-copyhelper
   (package
     (name "r-copyhelper")
@@ -1199,8 +1282,7 @@ GenomicRanges Bioconductor package.")
      `((upstream-name . "geneLenDataBase")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-rtracklayer" ,r-rtracklayer)
-       ("r-genomicfeatures" ,r-genomicfeatures)))
+     (list r-rtracklayer r-genomicfeatures))
     (home-page "https://bioconductor.org/packages/geneLenDataBase/")
     (synopsis "Lengths of mRNA transcripts for a number of genomes")
     (description
@@ -1225,7 +1307,7 @@ genomes and gene ID formats, largely based on the UCSC table browser.")
     ;; make sense to build substitutes.
     (arguments `(#:substitutable? #f))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
     (synopsis "Experimental data for use with the genomation package")
     (description
@@ -1240,18 +1322,13 @@ downloaded from Encode.")
     (version "1.14.0")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "http://bioconductor.org/packages/release/data/experiment"
-                    "/src/contrib/pasilla_" version ".tar.gz"))
+              (uri (bioconductor-uri "pasilla" version 'experiment))
               (sha256
                (base32
                 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocstyle" ,r-biocstyle)
-       ("r-dexseq" ,r-dexseq)
-       ("r-knitr" ,r-knitr)
-       ("r-rmarkdown" ,r-rmarkdown)))
+     (list r-biocstyle r-dexseq r-knitr r-rmarkdown))
     (home-page "https://www.bioconductor.org/packages/pasilla/")
     (synopsis "Data package with per-exon and per-gene read counts")
     (description "This package provides per-exon and per-gene read counts
@@ -1302,7 +1379,7 @@ resulting in a complete gene expression profile for each cell.")
     (properties `((upstream-name . "ALL")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)))
+     (list r-biobase))
     (home-page "https://bioconductor.org/packages/ALL")
     (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
     (description
@@ -1327,7 +1404,7 @@ the form of an @code{exprSet} object.")
     (properties `((upstream-name . "affydata")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)))
+     (list r-affy))
     (home-page "https://bioconductor.org/packages/affydata/")
     (synopsis "Affymetrix data for demonstration purposes")
     (description
@@ -1377,12 +1454,12 @@ yeast are also included.")
      `((upstream-name . "curatedTCGAData")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationhub" ,r-annotationhub)
-       ("r-experimenthub" ,r-experimenthub)
-       ("r-hdf5array" ,r-hdf5array)
-       ("r-multiassayexperiment" ,r-multiassayexperiment)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-annotationhub
+           r-experimenthub
+           r-hdf5array
+           r-multiassayexperiment
+           r-s4vectors
+           r-summarizedexperiment))
     (home-page "https://bioconductor.org/packages/curatedTCGAData/")
     (synopsis "Curated data from The Cancer Genome Atlas")
     (description
@@ -1395,20 +1472,39 @@ harmonized subsetting of rows (features) and columns (patients / samples)
 across the entire multi-'omics experiment.")
     (license license:artistic2.0)))
 
+(define-public r-tcgabiolinksgui-data
+  (package
+    (name "r-tcgabiolinksgui-data")
+    (version "1.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment))
+       (sha256
+        (base32 "08zmlvycq3jz1zy0715x9f21nf3465c51k7w2jq12sfbap36pmjm"))))
+    (properties `((upstream-name . "TCGAbiolinksGUI.data")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data")
+    (synopsis "Data for the TCGAbiolinksGUI package")
+    (description "This package provides supporting data for the
+TCGAbiolinksGUI package.")
+    (license license:gpl3)))
+
 
 ;;; Packages
 
 (define-public r-biocversion
   (package
     (name "r-biocversion")
-    (version "3.13.1")
+    (version "3.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocVersion" version))
        (sha256
         (base32
-         "0rsw8g4g1pcjw1zbx8x17yd3drhxqk4sx3cy3ddzy5731hl6mbfi"))))
+         "0qwzkh2alw7xhjprh719la0lg1q38pmjbipy3s2fy79m4xy8y8ik"))))
     (properties `((upstream-name . "BiocVersion")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BiocVersion/")
@@ -1421,13 +1517,13 @@ of Bioconductor.")
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.38.0")
+    (version "0.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "1kv7lzmyki3hi771v01nml1v1hzz8pyhqqv0xcdzqy354mlgx4m6"))))
+                "0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
@@ -1441,21 +1537,21 @@ packages.")
 (define-public r-coverageview
   (package
     (name "r-coverageview")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "CoverageView" version))
               (sha256
                (base32
-                "1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g"))))
+                "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-s4vectors" ,r-s4vectors)
-       ("r-iranges" ,r-iranges)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-rsamtools" ,r-rsamtools)))
+     (list r-s4vectors
+           r-iranges
+           r-genomicranges
+           r-genomicalignments
+           r-rtracklayer
+           r-rsamtools))
     (home-page "https://bioconductor.org/packages/CoverageView/")
     (synopsis "Coverage visualization package for R")
     (description "This package provides a framework for the visualization of
@@ -1468,25 +1564,25 @@ how the coverage distributed across the genome.")
 (define-public r-cummerbund
   (package
    (name "r-cummerbund")
-   (version "2.34.0")
+   (version "2.36.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "cummeRbund" version))
              (sha256
               (base32
-               "1avvmvrmldbscc7xd6a6k22xjykbzafvqf87wh5z9rx3qlzswsjx"))))
+               "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql"))))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-biobase" ,r-biobase)
-      ("r-biocgenerics" ,r-biocgenerics)
-      ("r-fastcluster" ,r-fastcluster)
-      ("r-ggplot2" ,r-ggplot2)
-      ("r-gviz" ,r-gviz)
-      ("r-plyr" ,r-plyr)
-      ("r-reshape2" ,r-reshape2)
-      ("r-rsqlite" ,r-rsqlite)
-      ("r-rtracklayer" ,r-rtracklayer)
-      ("r-s4vectors" ,r-s4vectors)))
+    (list r-biobase
+          r-biocgenerics
+          r-fastcluster
+          r-ggplot2
+          r-gviz
+          r-plyr
+          r-reshape2
+          r-rsqlite
+          r-rtracklayer
+          r-s4vectors))
    (home-page "https://bioconductor.org/packages/cummeRbund/")
    (synopsis "Analyze Cufflinks high-throughput sequencing data")
    (description "This package allows for persistent storage, access,
@@ -1495,24 +1591,54 @@ data.  In addition, provides numerous plotting functions for commonly
 used visualizations.")
    (license license:artistic2.0)))
 
+(define-public r-dearseq
+  (package
+    (name "r-dearseq")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "dearseq" version))
+       (sha256
+        (base32
+         "07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2
+           r-kernsmooth
+           r-matrixstats
+           r-patchwork
+           r-pbapply
+           r-statmod
+           r-survey
+           r-kernsmooth))
+    (home-page "https://github.com/borishejblum/dearseq")
+    (synopsis "DEA for RNA-seq data through a robust variance component test")
+    (description
+     "This is a package for Differential Expression Analysis of RNA-seq data.
+It features a variance component score test accounting for data
+heteroscedasticity through precision weights.  Perform both gene-wise and gene
+set analyses, and can deal with repeated or longitudinal data.")
+    (license license:gpl2)))
+
 (define-public r-decipher
   (package
     (name "r-decipher")
-    (version "2.20.0")
+    (version "2.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DECIPHER" version))
               (sha256
                (base32
-                "0mr7glkx2d37l9nszs52m0kycpm14vxl5gdp3z7i5j7yig1sw2nk"))))
+                "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-dbi" ,r-dbi)
-       ("r-iranges" ,r-iranges)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
+     (list r-biostrings
+           r-dbi
+           r-iranges
+           r-rsqlite
+           r-s4vectors
+           r-xvector))
     (home-page "https://www.bioconductor.org/packages/DECIPHER/")
     (synopsis "Tools for deciphering and managing biological sequences")
     (description "This package provides a toolset for deciphering and managing
@@ -1522,25 +1648,25 @@ biological sequences.")
 (define-public r-deepsnv
   (package
     (name "r-deepsnv")
-    (version "1.38.0")
+    (version "1.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "deepSNV" version))
               (sha256
                (base32
-                "0zz56hf417m7bgg2g2wpbaik30pi6h2nam1n5bviqgdn4mv8n0bs"))))
+                "1wi6j6yb6i9fs9yszfywqz3w50mhl85dkfmr4w3phwvkf0xkn81w"))))
     (properties `((upstream-name . "deepSNV")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)
-       ("r-vgam" ,r-vgam)))
+     (list r-biostrings
+           r-genomicranges
+           r-iranges
+           r-rhtslib
+           r-summarizedexperiment
+           r-variantannotation
+           r-vgam))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/gerstung-lab/deepSNV/")
     (synopsis "Detection of subclonal SNVs in deep sequencing data")
     (description
@@ -1558,24 +1684,21 @@ bases such as COSMIC.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.18.0")
+    (version "0.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "0w632262dqzcnvq9s6jvc7naz93dayx51fsv05s0zb6cjwygbqjr"))))
+                "1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixgenerics" ,r-matrixgenerics)))
+     (list r-biocgenerics r-s4vectors r-iranges r-matrix
+           r-matrixgenerics))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/DelayedArray")
     (synopsis "Delayed operations on array-like objects")
     (description
@@ -1588,28 +1711,88 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 @code{Matrix} objects, and ordinary arrays and data frames.")
     (license license:artistic2.0)))
 
+(define-public r-derfinderhelper
+  (package
+    (name "r-derfinderhelper")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "derfinderHelper" version))
+       (sha256
+        (base32 "06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35"))))
+    (properties `((upstream-name . "derfinderHelper")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-iranges r-matrix r-s4vectors))
+    (native-inputs
+     (list r-knitr))
+    (home-page "https://github.com/leekgroup/derfinderHelper")
+    (synopsis "Helper for derfinder")
+    (description
+     "This package speeds up the derfinder package when using multiple cores.
+It is particularly useful when using BiocParallel and it helps reduce the time
+spent loading the full derfinder package when running the F-statistics
+calculation in parallel.")
+    (license license:artistic2.0)))
+
+(define-public r-drimseq
+  (package
+    (name "r-drimseq")
+    (version "1.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DRIMSeq" version))
+       (sha256
+        (base32 "0y2jb0hb633id038zmwnfny6h4ai77fdyy02f77vha1z8xg5nl02"))))
+    (properties `((upstream-name . "DRIMSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biocparallel
+           r-edger
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-limma
+           r-mass
+           r-reshape2
+           r-s4vectors))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/DRIMSeq")
+    (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
+    (description
+     "The package provides two frameworks.  One for the differential
+transcript usage analysis between different conditions and one for the tuQTL
+analysis.  Both are based on modeling the counts of genomic features (i.e.,
+transcripts) with the Dirichlet-multinomial distribution.  The package also
+makes available functions for visualization and exploration of the data and
+results.")
+    (license license:gpl3+)))
+
 (define-public r-bluster
   (package
    (name "r-bluster")
-   (version "1.2.1")
+   (version "1.4.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "bluster" version))
             (sha256
              (base32
-              "128zd5vwlhmrkq0bpp1dxnkrcqfz1mjmdjlla4wqbjv7v6yyn6lg"))))
+              "1j24l12i3aga4qd827sj8b160yvrhlznggb4piddkmhjc0sppbjm"))))
    (properties `((upstream-name . "bluster")))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-biocneighbors" ,r-biocneighbors)
-      ("r-biocparallel" ,r-biocparallel)
-      ("r-cluster" ,r-cluster)
-      ("r-igraph" ,r-igraph)
-      ("r-matrix" ,r-matrix)
-      ("r-rcpp" ,r-rcpp)
-      ("r-s4vectors" ,r-s4vectors)))
+    (list r-biocneighbors
+          r-biocparallel
+          r-cluster
+          r-igraph
+          r-matrix
+          r-rcpp
+          r-s4vectors))
    (native-inputs
-    `(("r-knitr" ,r-knitr)))
+    (list r-knitr))
    (home-page "https://bioconductor.org/packages/bluster")
    (synopsis "Clustering algorithms for Bioconductor")
    (description"This package wraps common clustering algorithms in an easily
@@ -1621,21 +1804,21 @@ and evaluate clustering results.")
 (define-public r-ideoviz
   (package
     (name "r-ideoviz")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IdeoViz" version))
               (sha256
                (base32
-                "17sx0v5lq2zmg098ps4ksj1h0yla3vlh6s2w1ahqsq0nvm193scm"))))
+                "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-iranges" ,r-iranges)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-genomeinfodb" ,r-genomeinfodb)))
+     (list r-biobase
+           r-iranges
+           r-genomicranges
+           r-rcolorbrewer
+           r-rtracklayer
+           r-genomeinfodb))
     (home-page "https://bioconductor.org/packages/IdeoViz/")
     (synopsis "Plots data along a chromosomal ideogram")
     (description "This package provides functions to plot data associated with
@@ -1645,19 +1828,18 @@ arbitrary genomic intervals along chromosomal ideogram.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.26.0")
+    (version "2.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "0dzj8wqbjzilh2dsaj3ylx958xqrv0c688ayfq2r1z7rs75qy7kx"))))
+                "07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocgenerics r-s4vectors))
     (home-page "https://bioconductor.org/packages/IRanges")
     (synopsis "Infrastructure for manipulating intervals on sequences")
     (description
@@ -1671,6 +1853,59 @@ naming and share the same rich and consistent \"Vector API\" as much as
 possible.")
     (license license:artistic2.0)))
 
+(define-public r-isoformswitchanalyzer
+  (package
+    (name "r-isoformswitchanalyzer")
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
+       (sha256
+        (base32 "14bqf39gw5ab5r9sr3afkig1jbzdvds1bmcvc6bpb45kschx7fwf"))))
+    (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-biocgenerics
+           r-biostrings
+           r-bsgenome
+           r-dbi
+           r-dexseq
+           r-dplyr
+           r-drimseq
+           r-edger
+           r-futile-logger
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-gridextra
+           r-iranges
+           r-limma
+           r-magrittr
+           r-plyr
+           r-rcolorbrewer
+           r-rcurl
+           r-readr
+           r-reshape2
+           r-rtracklayer
+           r-stringr
+           r-tibble
+           r-tximeta
+           r-tximport
+           r-venndiagram
+           r-xvector))
+    (native-inputs
+     (list r-knitr))
+    (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
+    (synopsis "Analyze alternative splicing in RNA-seq data")
+    (description
+     "This is a package for the analysis of alternative splicing and isoform
+switches with predicted functional consequences (e.g. gain/loss of protein
+domains etc.) from quantification of all types of RNASeq by tools such as
+Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
+    (license license:gpl2+)))
+
 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
 (define-public r-absfiltergsea
   (package
@@ -1685,11 +1920,7 @@ possible.")
     (properties `((upstream-name . "AbsFilterGSEA")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-deseq" ,r-deseq)
-       ("r-limma" ,r-limma)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+     (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
     (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
     (synopsis "Improved false positive control of gene-permuting with absolute filtering")
     (description
@@ -1713,10 +1944,9 @@ absolute GSEA.")
    (properties `((upstream-name . "BisqueRNA")))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-biobase" ,r-biobase)
-      ("r-limsolve" ,r-limsolve)))
+    (list r-biobase r-limsolve))
    (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
    (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
    (synopsis "Decomposition of bulk expression with single-cell sequencing")
    (description "This package provides tools to accurately estimate cell type
@@ -1743,10 +1973,8 @@ relative abundances across samples.")
      `((upstream-name . "deconstructSigs")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-reshape2" ,r-reshape2)))
+     (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
+           r-reshape2))
     (home-page "https://github.com/raerose01/deconstructSigs")
     (synopsis "Identifies signatures present in a tumor sample")
     (description "This package takes sample information in the form of the
@@ -1756,6 +1984,33 @@ closely reconstructs the mutational profile.")
     (license license:gpl2+)))
 
 ;; This is a CRAN package, but it depends on Bioconductor packages.
+(define-public r-jetset
+  (package
+    (name "r-jetset")
+    (version "3.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "jetset" version))
+       (sha256
+        (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
+    (properties `((upstream-name . "jetset")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
+    (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
+    (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
+    (description
+     "This package provides a one-to-one mapping from gene to \"best\" probe
+set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
+hgu133plus2, and u133x3p.  On Affymetrix gene expression microarrays, a single
+gene may be measured by multiple probe sets.  This can present a mild
+conundrum when attempting to evaluate a gene \"signature\" that is defined by
+gene names rather than by specific probe sets.  This package also includes the
+pre-calculated probe set quality scores that were used to define the
+mapping.")
+    (license license:artistic2.0)))
+
+;; This is a CRAN package, but it depends on Bioconductor packages.
 (define-public r-nmf
   (package
     (name "r-nmf")
@@ -1770,25 +2025,25 @@ closely reconstructs the mutational profile.")
     (properties `((upstream-name . "NMF")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-cluster" ,r-cluster)
-       ("r-biobase" ,r-biobase)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-bigmemory" ,r-bigmemory) ; suggested
-       ("r-synchronicity" ,r-synchronicity) ; suggested
-       ("r-colorspace" ,r-colorspace)
-       ("r-digest" ,r-digest)
-       ("r-doparallel" ,r-doparallel)
-       ("r-foreach" ,r-foreach)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridbase" ,r-gridbase)
-       ("r-pkgmaker" ,r-pkgmaker)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-registry" ,r-registry)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rngtools" ,r-rngtools)
-       ("r-stringr" ,r-stringr)))
+     (list r-cluster
+           r-biobase
+           r-biocmanager
+           r-bigmemory ; suggested
+           r-synchronicity ; suggested
+           r-colorspace
+           r-digest
+           r-doparallel
+           r-foreach
+           r-ggplot2
+           r-gridbase
+           r-pkgmaker
+           r-rcolorbrewer
+           r-registry
+           r-reshape2
+           r-rngtools
+           r-stringr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "http://renozao.github.io/NMF")
     (synopsis "Algorithms and framework for nonnegative matrix factorization")
     (description
@@ -1803,24 +2058,24 @@ performing parallel computations on multicore machines.")
 (define-public r-affy
   (package
     (name "r-affy")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affy" version))
        (sha256
         (base32
-         "0vz5y92gqcm0qk57qlba85bk683lzdr7vkmxv109rq6i17vdkkrm"))))
+         "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affyio" ,r-affyio)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-preprocesscore" ,r-preprocesscore)
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list r-affyio
+           r-biobase
+           r-biocgenerics
+           r-biocmanager
+           r-preprocesscore
+           r-zlibbioc))
     (inputs
-     `(("zlib" ,zlib)))
+     (list zlib))
     (home-page "https://bioconductor.org/packages/affy")
     (synopsis "Methods for affymetrix oligonucleotide arrays")
     (description
@@ -1831,17 +2086,17 @@ analysis.")
 (define-public r-affycomp
   (package
     (name "r-affycomp")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycomp" version))
        (sha256
         (base32
-         "07my5scdh6h0y1bx1h9y5m4fa8bnmw389f83gkb7cf19w4vp36b2"))))
+         "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21"))))
     (properties `((upstream-name . "affycomp")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-biobase" ,r-biobase)))
+    (propagated-inputs (list r-biobase))
     (home-page "https://bioconductor.org/packages/affycomp/")
     (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
     (description
@@ -1852,21 +2107,19 @@ measures for Affymetrix Oligonucleotide Arrays.")
 (define-public r-affycompatible
   (package
     (name "r-affycompatible")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AffyCompatible" version))
        (sha256
         (base32
-         "1xwz22wf2smsvmd0d5lfadbsgscnl3fl9msypy2mml38k048p6vj"))))
+         "1qlfh1gcwa6akd5dhdqh260yaw1j6dap6a15ghwf74rchi5218sg"))))
     (properties
      `((upstream-name . "AffyCompatible")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-rcurl" ,r-rcurl)
-       ("r-xml" ,r-xml)))
+     (list r-biostrings r-rcurl r-xml))
     (home-page "https://bioconductor.org/packages/AffyCompatible/")
     (synopsis "Work with Affymetrix GeneChip files")
     (description
@@ -1880,20 +2133,18 @@ Command Console} (AGCC)-compatible sample annotation files.")
 (define-public r-affycontam
   (package
     (name "r-affycontam")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyContam" version))
        (sha256
         (base32
-         "0242ga68wrdk1kcmxfdbq73a0d3zhrzdlzkzphfg3q0zjbvg49jj"))))
+         "1vw3nxg9jvlw0zg9h70w2ww8l42qpyvgf12hsla9hyyfhj3m6i9f"))))
     (properties `((upstream-name . "affyContam")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-affydata" ,r-affydata)
-       ("r-biobase" ,r-biobase)))
+     (list r-affy r-affydata r-biobase))
     (home-page "https://bioconductor.org/packages/affyContam/")
     (synopsis "Structured corruption of Affymetrix CEL file data")
     (description
@@ -1905,38 +2156,38 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
 (define-public r-affycoretools
   (package
     (name "r-affycoretools")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycoretools" version))
        (sha256
         (base32
-         "1dx861spr3kn1dxwhf43s5l1r7bmrq0h6538l3q64iiwzzc6krdh"))))
+         "1ccyaj129ii9f47r41qsy34y6ck4wna55j8vz3v3hbldddn93f40"))))
     (properties `((upstream-name . "affycoretools")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-dbi" ,r-dbi)
-       ("r-edger" ,r-edger)
-       ("r-gcrma" ,r-gcrma)
-       ("r-glimma" ,r-glimma)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gostats" ,r-gostats)
-       ("r-gplots" ,r-gplots)
-       ("r-hwriter" ,r-hwriter)
-       ("r-lattice" ,r-lattice)
-       ("r-limma" ,r-limma)
-       ("r-oligoclasses" ,r-oligoclasses)
-       ("r-reportingtools" ,r-reportingtools)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xtable" ,r-xtable)))
+     (list r-affy
+           r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-dbi
+           r-edger
+           r-gcrma
+           r-glimma
+           r-ggplot2
+           r-gostats
+           r-gplots
+           r-hwriter
+           r-lattice
+           r-limma
+           r-oligoclasses
+           r-reportingtools
+           r-rsqlite
+           r-s4vectors
+           r-xtable))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/affycoretools/")
     (synopsis "Functions for analyses with Affymetrix GeneChips")
     (description
@@ -1947,19 +2198,19 @@ to streamline the more common analyses that a Biostatistician might see.")
 (define-public r-affyio
   (package
     (name "r-affyio")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyio" version))
        (sha256
         (base32
-         "07kibqsm888g06qqqa4648ph877kriy74kprbri8nyx83y8aspjr"))))
+         "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-zlibbioc" ,r-zlibbioc)))
+     (list r-zlibbioc))
     (inputs
-     `(("zlib" ,zlib)))
+     (list zlib))
     (home-page "https://github.com/bmbolstad/affyio")
     (synopsis "Tools for parsing Affymetrix data files")
     (description
@@ -1971,14 +2222,14 @@ CDF file formats.")
 (define-public r-affxparser
   (package
     (name "r-affxparser")
-    (version "1.64.1")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affxparser" version))
        (sha256
         (base32
-         "0lr0kmp087j2g4i5kd7rh8a038ymp6z82861lyql2fwk5dh80043"))))
+         "1bd0f8ifj6l7dx2m3wpmd0mji2gdf39mzgcjf9lbvvmbqnbxbcal"))))
     (properties `((upstream-name . "affxparser")))
     (build-system r-build-system)
     (home-page "https://github.com/HenrikBengtsson/affxparser")
@@ -1999,23 +2250,23 @@ structure.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "13ny596wh65sw7dbw0zd4h84d6k1w99g91c4sqy83mdzgpv73sz7"))))
+         "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-dbi" ,r-dbi)
-       ("r-httr" ,r-httr)
-       ("r-xml" ,r-xml)
-       ("r-xtable" ,r-xtable)))
+     (list r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-dbi
+           r-httr
+           r-xml
+           r-xtable))
     (home-page
      "https://bioconductor.org/packages/annotate")
     (synopsis "Annotation for microarrays")
@@ -2026,26 +2277,26 @@ microarrays.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.54.1")
+    (version "1.56.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "0fcammls431pgmp47r85k0zh3bz42bajbqdmafd31kpqncc1ijal"))))
+                "01zwq14msbbwzxv8rgpmyr74ymvhq0vnmxkxxwd886iac5vjlgi8"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-dbi" ,r-dbi)
-       ("r-keggrest" ,r-keggrest)
-       ("r-iranges" ,r-iranges)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biobase
+           r-biocgenerics
+           r-dbi
+           r-keggrest
+           r-iranges
+           r-rsqlite
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/AnnotationDbi")
     (synopsis "Annotation database interface")
     (description
@@ -2056,21 +2307,20 @@ annotation data packages using SQLite data storage.")
 (define-public r-annotationfilter
   (package
     (name "r-annotationfilter")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationFilter" version))
               (sha256
                (base32
-                "0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa"))))
+                "15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w"))))
     (properties
      `((upstream-name . "AnnotationFilter")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-genomicranges" ,r-genomicranges)
-       ("r-lazyeval" ,r-lazyeval)))
+     (list r-genomicranges r-lazyeval))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/Bioconductor/AnnotationFilter")
     (synopsis "Facilities for filtering Bioconductor annotation resources")
     (description
@@ -2082,28 +2332,28 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax"))))
+         "02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-dbi" ,r-dbi)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xml" ,r-xml)))
+     (list r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-dbi
+           r-rcurl
+           r-rsqlite
+           r-s4vectors
+           r-xml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/AnnotationForge")
     (synopsis "Code for building annotation database packages")
     (description
@@ -2114,32 +2364,32 @@ databases.  Packages produced are intended to be used with AnnotationDbi.")
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-    (version "3.0.1")
+    (version "3.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHub" version))
        (sha256
         (base32
-         "12i8lafy1z97gs4knqi7r5l1hd7dr6j8a23qj4fkdpqsdpyz21z7"))))
+         "0ks8yzvvs2r66pb9687mkskf0n3wgvp7h92k83b0a1q32sca5wng"))))
     (properties `((upstream-name . "AnnotationHub")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biocversion" ,r-biocversion)
-       ("r-curl" ,r-curl)
-       ("r-dplyr" ,r-dplyr)
-       ("r-httr" ,r-httr)
-       ("r-interactivedisplaybase" ,r-interactivedisplaybase)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-yaml" ,r-yaml)))
+     (list r-annotationdbi
+           r-biocfilecache
+           r-biocgenerics
+           r-biocmanager
+           r-biocversion
+           r-curl
+           r-dplyr
+           r-httr
+           r-interactivedisplaybase
+           r-rappdirs
+           r-rsqlite
+           r-s4vectors
+           r-yaml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/AnnotationHub")
     (synopsis "Client to access AnnotationHub resources")
     (description
@@ -2155,21 +2405,18 @@ by the user, helping with quick and reproducible access.")
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-    (version "3.22.0")
+    (version "3.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "aroma.light" version))
        (sha256
         (base32
-         "1yvq6l1p8cpijvlib4fn9y88ihn0gaalrmgx82jgrfmnszkqn3y5"))))
+         "12qa85hsp8d1xhgn27iymknbhpnp9bd7hsgqxwvp1i8kki06z5hp"))))
     (properties `((upstream-name . "aroma.light")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-matrixstats" ,r-matrixstats)
-       ("r-r-methodss3" ,r-r-methodss3)
-       ("r-r-oo" ,r-r-oo)
-       ("r-r-utils" ,r-r-utils)))
+     (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
     (home-page "https://github.com/HenrikBengtsson/aroma.light")
     (synopsis "Methods for normalization and visualization of microarray data")
     (description
@@ -2182,24 +2429,24 @@ classes.")
 (define-public r-bamsignals
   (package
     (name "r-bamsignals")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bamsignals" version))
        (sha256
         (base32
-         "1ljrip0jlxjcljqac7vzvwqbcqil5v4f4s4bhpq4akvdkshas6mn"))))
+         "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list r-biocgenerics
+           r-genomicranges
+           r-iranges
+           r-rcpp
+           r-rhtslib
+           r-zlibbioc))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/bamsignals")
     (synopsis "Extract read count signals from bam files")
     (description
@@ -2212,18 +2459,18 @@ paired-end data.")
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.52.0")
+    (version "2.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "1sg8w8860zhlz9s1pf75xa8asd2hyqsj13fh5xc37hf5yqdfkavr"))))
+                "0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)))
+     (list r-biocgenerics))
     (home-page "https://bioconductor.org/packages/Biobase")
     (synopsis "Base functions for Bioconductor")
     (description
@@ -2234,28 +2481,28 @@ on Bioconductor or which replace R functions.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.48.3")
+    (version "2.50.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "096s243yzbhhz3wsm7azml5sznqczmcpi5g0gnb02mah1przczfx"))))
+                "1lm8axjmi2k1d2x0gdlvs0fzsd68xvxx7sn1wn6v4wr0pv85qhkz"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-digest" ,r-digest)
-       ("r-httr" ,r-httr)
-       ("r-progress" ,r-progress)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-stringr" ,r-stringr)
-       ("r-xml" ,r-xml)
-       ("r-xml2" ,r-xml2)))
+     (list r-annotationdbi
+           r-biocfilecache
+           r-digest
+           r-httr
+           r-progress
+           r-rappdirs
+           r-stringr
+           r-xml
+           r-xml2))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/biomaRt")
     (synopsis "Interface to BioMart databases")
     (description
@@ -2272,13 +2519,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.26.2")
+    (version "1.28.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "1y459cygq21f3igsdlxz1zlyad8qbl2qlr5h2d2dpnvblykvf48i"))))
+                "0lkp7m2l66zq8yl788mkvi9kpb1haywxpf6ip9xl5y6iwm1w2b8p"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -2306,16 +2553,14 @@ powerful online queries from gene annotation to database mining.")
                (("\\today") "later"))
 
              ;; Initialize the random number generator seed when building.
-             (substitute* "R/internal_rng_stream.R"
+             (substitute* "R/rng.R"
                (("\"L'Ecuyer-CMRG\"\\)" m)
                 (string-append
                  m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
     (propagated-inputs
-     `(("r-futile-logger" ,r-futile-logger)
-       ("r-snow" ,r-snow)
-       ("r-bh" ,r-bh)))
+     (list r-futile-logger r-snow r-bh))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiocParallel")
     (synopsis "Bioconductor facilities for parallel evaluation")
     (description
@@ -2327,23 +2572,23 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.60.2")
+    (version "2.62.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "0ai0fg0w4l0a7avbafdbqjgjpg91myxalwrg2i3ixm1l2lyyfyah"))))
+                "11qkw863mkfz3mc55v2gmfr4w3xziqfb5pq3hmjqpn8vpw8ax3xq"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-crayon" ,r-crayon)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
+     (list r-biocgenerics
+           r-crayon
+           r-genomeinfodb
+           r-iranges
+           r-s4vectors
+           r-xvector))
     (home-page "https://bioconductor.org/packages/Biostrings")
     (synopsis "String objects and algorithms for biological sequences")
     (description
@@ -2355,36 +2600,36 @@ biological sequences or sets of sequences.")
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biovizBase" version))
        (sha256
         (base32
-         "14jyyg3ggdhaqhp0j4qf6dapykh76fygbaa4lr7czqbc5mr0iw23"))))
+         "0kg71p7sqfvxal0c19zrws1ffaqgyi8p605l3z6mkq5ldi26pajz"))))
     (properties `((upstream-name . "biovizBase")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationfilter" ,r-annotationfilter)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dichromat" ,r-dichromat)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-hmisc" ,r-hmisc)
-       ("r-iranges" ,r-iranges)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rlang" ,r-rlang)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-annotationdbi
+           r-annotationfilter
+           r-biocgenerics
+           r-biostrings
+           r-dichromat
+           r-ensembldb
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-hmisc
+           r-iranges
+           r-rcolorbrewer
+           r-rlang
+           r-rsamtools
+           r-s4vectors
+           r-scales
+           r-summarizedexperiment
+           r-variantannotation))
     (home-page "https://bioconductor.org/packages/biovizBase")
     (synopsis "Basic graphic utilities for visualization of genomic data")
     (description
@@ -2397,27 +2642,27 @@ effort and encourages consistency.")
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.60.0")
+    (version "1.62.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "1jhissp9ad1rn2p0bzr3yslbn84yqbaqgnn5p9hyacwr7mr091cn"))))
+                "1b023dpy8ygq0kd6qy0mk97c66gzpf39y2s0n89kmv61z5sg0jyi"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
+     (list r-biocgenerics
+           r-biostrings
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-matrixstats
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-xvector))
     (home-page "https://bioconductor.org/packages/BSgenome")
     (synopsis "Infrastructure for Biostrings-based genome data packages")
     (description
@@ -2428,27 +2673,27 @@ genome data packages and support for efficient SNP representation.")
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.58.0")
+    (version "2.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "0f76pb7h8qc51mca5pq00m9p02sbkcj6ywfzli20qai2ykpfr71x"))))
+         "164zp4la9rqnp5vpn2y2p6plc5yxyk2kmn0z3d2flla54zc1b427"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genefilter" ,r-genefilter)
-       ("r-graph" ,r-graph)
-       ("r-gseabase" ,r-gseabase)
-       ("r-matrix" ,r-matrix)
-       ("r-rbgl" ,r-rbgl)
-       ("r-dbi" ,r-dbi)))
+     (list r-annotate
+           r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-genefilter
+           r-graph
+           r-gseabase
+           r-matrix
+           r-rbgl
+           r-dbi))
     (home-page "https://bioconductor.org/packages/Category")
     (synopsis "Category analysis")
     (description
@@ -2459,37 +2704,36 @@ analysis.")
 (define-public r-chipseeker
   (package
     (name "r-chipseeker")
-    (version "1.28.3")
+    (version "1.30.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ChIPseeker" version))
               (sha256
                (base32
-                "18hdgml80770c0xgd06zrl8px1ql9fa65rirfkq07z7rzpnd23rw"))))
+                "1f9m1p1viiigkmv15r2mknjrfw047jw1fylpqz5ipigc3jrphj1g"))))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-boot" ,r-boot)
-       ("r-enrichplot" ,r-enrichplot)
-       ("r-iranges" ,r-iranges)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gplots" ,r-gplots)
-       ("r-gtools" ,r-gtools)
-       ("r-dplyr" ,r-dplyr)
-       ("r-plotrix" ,r-plotrix)
-       ("r-dplyr" ,r-dplyr)
-       ("r-magrittr" ,r-magrittr)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-txdb-hsapiens-ucsc-hg19-knowngene"
-        ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
+     (list r-annotationdbi
+           r-biocgenerics
+           r-boot
+           r-enrichplot
+           r-iranges
+           r-genomeinfodb
+           r-genomicranges
+           r-genomicfeatures
+           r-ggplot2
+           r-gplots
+           r-gtools
+           r-dplyr
+           r-plotrix
+           r-dplyr
+           r-magrittr
+           r-rcolorbrewer
+           r-rtracklayer
+           r-s4vectors
+           r-txdb-hsapiens-ucsc-hg19-knowngene))
     (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
     (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
     (description "This package implements functions to retrieve the nearest
@@ -2506,22 +2750,22 @@ annotation, distance to TSS, and overlap of peaks or genes.")
 (define-public r-chipseq
   (package
     (name "r-chipseq")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chipseq" version))
        (sha256
         (base32
-         "078p9h0zghlhpd6cr54nww1mk7q97imx8yqfayw5m2yq4097ivbi"))))
+         "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shortread" ,r-shortread)))
+     (list r-biocgenerics
+           r-genomicranges
+           r-iranges
+           r-lattice
+           r-s4vectors
+           r-shortread))
     (home-page "https://bioconductor.org/packages/chipseq")
     (synopsis "Package for analyzing ChIPseq data")
     (description
@@ -2532,33 +2776,32 @@ experiments.")
 (define-public r-complexheatmap
   (package
     (name "r-complexheatmap")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ComplexHeatmap" version))
        (sha256
         (base32
-         "0jl96msj1njdrvngg68s50vmphvhi2lfwlv34x07pcdzgkjjs41f"))))
+         "124w74mk0zk035wyr7cimblzx5blags4n5c8f83mp7iimxcb4gcn"))))
     (properties
      `((upstream-name . "ComplexHeatmap")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-cairo" ,r-cairo)
-       ("r-circlize" ,r-circlize)
-       ("r-clue" ,r-clue)
-       ("r-colorspace" ,r-colorspace)
-       ("r-digest" ,r-digest)
-       ("r-doparallel" ,r-doparallel)
-       ("r-foreach" ,r-foreach)
-       ("r-getoptlong" ,r-getoptlong)
-       ("r-globaloptions" ,r-globaloptions)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-png" ,r-png)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+     (list r-circlize
+           r-clue
+           r-colorspace
+           r-digest
+           r-doparallel
+           r-foreach
+           r-getoptlong
+           r-globaloptions
+           r-iranges
+           r-matrixstats
+           r-png
+           r-rcolorbrewer))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page
      "https://github.com/jokergoo/ComplexHeatmap")
     (synopsis "Making Complex Heatmaps")
@@ -2572,31 +2815,31 @@ self-defined annotation graphics.")
 (define-public r-copywriter
   (package
     (name "r-copywriter")
-    (version "2.24.0")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CopywriteR" version))
        (sha256
         (base32
-         "0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp"))))
+         "0xm5gjzi4r1xzyn7r669blqxhyhmbk9rh9k2gn696j14hbhc1hcy"))))
     (properties `((upstream-name . "CopywriteR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-chipseq" ,r-chipseq)
-       ("r-copyhelper" ,r-copyhelper)
-       ("r-data-table" ,r-data-table)
-       ("r-dnacopy" ,r-dnacopy)
-       ("r-futile-logger" ,r-futile-logger)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gtools" ,r-gtools)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocparallel
+           r-chipseq
+           r-copyhelper
+           r-data-table
+           r-dnacopy
+           r-futile-logger
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-gtools
+           r-iranges
+           r-matrixstats
+           r-rsamtools
+           r-s4vectors))
     (home-page "https://github.com/PeeperLab/CopywriteR")
     (synopsis "Copy number information from targeted sequencing")
     (description
@@ -2623,14 +2866,14 @@ number detection tools.")
     (properties `((upstream-name . "DESeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genefilter" ,r-genefilter)
-       ("r-geneplotter" ,r-geneplotter)
-       ("r-lattice" ,r-lattice)
-       ("r-locfit" ,r-locfit)
-       ("r-mass" ,r-mass)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+     (list r-biobase
+           r-biocgenerics
+           r-genefilter
+           r-geneplotter
+           r-lattice
+           r-locfit
+           r-mass
+           r-rcolorbrewer))
     (home-page "https://www-huber.embl.de/users/anders/DESeq/")
     (synopsis "Differential gene expression analysis")
     (description
@@ -2643,32 +2886,32 @@ distribution.")
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "0r1brwmj7av0bj72jajn27vx3zs1bgg8qfbhf02fln6kf7im4kaz"))))
+         "0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-genefilter" ,r-genefilter)
-       ("r-geneplotter" ,r-geneplotter)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-locfit" ,r-locfit)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-genefilter
+           r-geneplotter
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-locfit
+           r-rcpp
+           r-rcpparmadillo
+           r-s4vectors
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/DESeq2")
     (synopsis "Differential gene expression analysis")
     (description
@@ -2681,36 +2924,36 @@ distribution.")
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "1zywh30f4j4rj0f9w6yk5xr9mvdbg8gicy3wsb8yxdnamadyr7x4"))))
+         "1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biomart" ,r-biomart)
-       ("r-deseq2" ,r-deseq2)
-       ("r-genefilter" ,r-genefilter)
-       ("r-geneplotter" ,r-geneplotter)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-hwriter" ,r-hwriter)
-       ("r-iranges" ,r-iranges)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-statmod" ,r-statmod)
-       ("r-stringr" ,r-stringr)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-biomart
+           r-deseq2
+           r-genefilter
+           r-geneplotter
+           r-genomicranges
+           r-hwriter
+           r-iranges
+           r-rcolorbrewer
+           r-rsamtools
+           r-s4vectors
+           r-statmod
+           r-stringr
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/DEXSeq")
     (synopsis "Inference of differential exon usage in RNA-Seq")
     (description
@@ -2726,23 +2969,21 @@ exploration of the results.")
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DirichletMultinomial" version))
        (sha256
         (base32
-         "0ikmj0300lfzj6q1vyahfyx5kwi5h59mds7ym4f2j1bbxqzy6ssl"))))
+         "06nallp9jj2vmaa7d18g6hiymjc109szdv8sp51r87n7s38bvyq6"))))
     (properties
      `((upstream-name . "DirichletMultinomial")))
     (build-system r-build-system)
     (inputs
-     `(("gsl" ,gsl)))
+     (list gsl))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocgenerics r-iranges r-s4vectors))
     (home-page "https://bioconductor.org/packages/DirichletMultinomial")
     (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
     (description
@@ -2755,31 +2996,31 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-    (version "2.26.1")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EDASeq" version))
        (sha256
         (base32
-         "0pakcbkalhhqz3d9lpfx3hscf53k24mlmrywxxzfg43yq57srkql"))))
+         "1vygfdxbjcww7sqzc3j7sp7w13dx10vlzy9z31flf7345qp6blj7"))))
     (properties `((upstream-name . "EDASeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-aroma-light" ,r-aroma-light)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-shortread" ,r-shortread)))
+     (list r-annotationdbi
+           r-aroma-light
+           r-biobase
+           r-biocgenerics
+           r-biocmanager
+           r-biomart
+           r-biostrings
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-rsamtools
+           r-shortread))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/drisso/EDASeq")
     (synopsis "Exploratory data analysis and normalization for RNA-Seq")
     (description
@@ -2795,20 +3036,17 @@ global-scaling and full-quantile normalization.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.34.1")
+    (version "3.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0f6apsjq6cn794840ls9y2n0hix1gyhvkdgxch1v22qr4sq0c86k"))))
+                "1d18kdfi9vjhhw5kwfy5airrd3c16fh4wbwppbhwgawm038mwavk"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-limma" ,r-limma)
-       ("r-locfit" ,r-locfit)
-       ("r-rcpp" ,r-rcpp)
-       ("r-statmod" ,r-statmod))) ;for estimateDisp
+     (list r-limma r-locfit r-rcpp r-statmod)) ;for estimateDisp
     (home-page "http://bioinf.wehi.edu.au/edgeR")
     (synopsis "EdgeR does empirical analysis of digital gene expression data")
     (description "This package can do differential expression analysis of
@@ -2823,34 +3061,34 @@ CAGE.")
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.16.4")
+    (version "2.18.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "15yllkxr6sj5pfvkvv285nk3q5374nzq1iz8ywmnrq910k3xagd8"))))
+         "0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationfilter" ,r-annotationfilter)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-curl" ,r-curl)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-annotationdbi
+           r-annotationfilter
+           r-biobase
+           r-biocgenerics
+           r-biostrings
+           r-curl
+           r-dbi
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-protgenerics
+           r-rsamtools
+           r-rsqlite
+           r-rtracklayer
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/jotsetung/ensembldb")
     (synopsis "Utilities to create and use Ensembl-based annotation databases")
     (description
@@ -2868,21 +3106,18 @@ chromosome region or transcript models of lincRNA genes.")
 (define-public r-fastseg
   (package
     (name "r-fastseg")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fastseg" version))
        (sha256
         (base32
-         "006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0"))))
+         "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biobase r-biocgenerics r-genomicranges r-iranges
+           r-s4vectors))
     (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
     (synopsis "Fast segmentation algorithm for genetic sequencing data")
     (description
@@ -2898,20 +3133,17 @@ microarrays or GRanges for sequencing data.")
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.42.0")
+    (version "2.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "0z7hrwdm6my6p7z04bcpfhqk72pd0s1bdzvsiiym59qj79fbvb83"))))
+         "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-go-db" ,r-go-db)
-       ("r-graph" ,r-graph)
-       ("r-keggrest" ,r-keggrest)))
+     (list r-annotationdbi r-go-db r-graph r-keggrest))
     (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
                               "articles/10.1186/1471-2105-10-161"))
     (synopsis "Generally applicable gene-set enrichment for pathway analysis")
@@ -2929,24 +3161,20 @@ analysis using other methods.")
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk"))))
+         "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2"))))
     (build-system r-build-system)
     (native-inputs
-     `(("gfortran" ,gfortran)
-       ("r-knitr" ,r-knitr)))
+     (list gfortran r-knitr))
     (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-survival" ,r-survival)))
+     (list r-annotate r-annotationdbi r-biobase r-biocgenerics
+           r-survival))
     (home-page "https://bioconductor.org/packages/genefilter")
     (synopsis "Filter genes from high-throughput experiments")
     (description
@@ -2957,17 +3185,16 @@ high-throughput sequencing experiments.")
 (define-public r-geneoverlap
   (package
     (name "r-geneoverlap")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GeneOverlap" version))
               (sha256
                (base32
-                "1kfw3h68rvbafhklds6sfmviwv91nms8wk0ywzkjg5h3mmgxbsv9"))))
+                "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-gplots" ,r-gplots)))
+     (list r-rcolorbrewer r-gplots))
     (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
     (synopsis "Test and visualize gene overlaps")
     (description "This package can be used to test two sets of gene lists
@@ -2977,37 +3204,37 @@ and visualize the results.")
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "0qa3b4mfd7l1sy4pw64zr2d90y5apah900krxjl4x39acygg0i2r"))))
+                "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-data-table" ,r-data-table)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridbase" ,r-gridbase)
-       ("r-impute" ,r-impute)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-plotrix" ,r-plotrix)
-       ("r-plyr" ,r-plyr)
-       ("r-rcpp" ,r-rcpp)
-       ("r-readr" ,r-readr)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-seqpattern" ,r-seqpattern)))
+     (list r-biostrings
+           r-bsgenome
+           r-data-table
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-gridbase
+           r-impute
+           r-iranges
+           r-matrixstats
+           r-plotrix
+           r-plyr
+           r-rcpp
+           r-readr
+           r-reshape2
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-seqpattern))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
     (synopsis "Summary, annotation and visualization of genomic data")
     (description
@@ -3024,24 +3251,21 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.28.4")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "0fjpgvpvyvl8cqgh2annib6h0c5li3aqz1ajfh5z5k5d0avdm4w0"))))
+                "1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomeinfodbdata" ,r-genomeinfodbdata)
-       ("r-iranges" ,r-iranges)
-       ("r-rcurl" ,r-rcurl)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/GenomeInfoDb")
     (synopsis "Utilities for manipulating chromosome identifiers")
     (description
@@ -3054,26 +3278,26 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "00rq110jkh89nxgk05zh8kssxk8mb4dq0wjg3n7ivfmmm9wdwhp2"))))
+                "1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-rsamtools
+           r-s4vectors
+           r-summarizedexperiment))
     (home-page "https://bioconductor.org/packages/GenomicAlignments")
     (synopsis "Representation and manipulation of short genomic alignments")
     (description
@@ -3087,34 +3311,34 @@ alignments.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.44.2")
+    (version "1.46.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "091p8xnf2xkqhind81vyv1rmy2fz2b3qalcbrsw4qnp24vgdv2am"))))
+                "0a3shdzc1r0f12q9w679hgj8ywrwbg36z7k0yp47dgfjl14lachk"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocio" ,r-biocio)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
+     (list r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-biocio
+           r-biomart
+           r-biostrings
+           r-dbi
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-rcurl
+           r-rsqlite
+           r-rtracklayer
+           r-s4vectors
+           r-xvector))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/GenomicFeatures")
     (synopsis "Tools for working with transcript centric annotations")
     (description
@@ -3131,29 +3355,29 @@ extracting the desired features in a convenient format.")
 (define-public r-genomicfiles
   (package
     (name "r-genomicfiles")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicFiles" version))
        (sha256
         (base32
-         "1plh14m7w6calw5yxcxp7g4bg8q00ax85m517wap78bni975k13y"))))
+         "0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x"))))
     (properties `((upstream-name . "GenomicFiles")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixgenerics" ,r-matrixgenerics)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-biocgenerics
+           r-biocparallel
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-iranges
+           r-matrixgenerics
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-summarizedexperiment
+           r-variantannotation))
     (home-page "https://bioconductor.org/packages/GenomicFiles")
     (synopsis "Distributed computing by file or by range")
     (description
@@ -3165,24 +3389,20 @@ provide added flexibility for data combination and manipulation.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.44.0")
+    (version "1.46.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "1qxc6dcwdlkan3hg0j9yfhz7gyi9qg671yj6zizsk6mzl7qqva0x"))))
+                "133r27wsdyppjv9kq0d2xamx007lkf416nnlaygs4hs3a76p9xwx"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
+     (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/GenomicRanges")
     (synopsis "Representation and manipulation of genomic intervals")
     (description
@@ -3196,26 +3416,26 @@ manipulating genomic intervals and variables defined along a genome.")
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.58.0")
+    (version "2.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "0jjswy6qmfgr2f6vk3y9pdvs9x91gn31h55qllgh0qb2cb26g9wa"))))
+         "1f8wqdl0swnvs59i6ljjcaglfqv314n8zxy4crpx806gbjzpn76z"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationforge" ,r-annotationforge)
-       ("r-biobase" ,r-biobase)
-       ("r-category" ,r-category)
-       ("r-go-db" ,r-go-db)
-       ("r-graph" ,r-graph)
-       ("r-rgraphviz" ,r-rgraphviz)
-       ("r-rbgl" ,r-rbgl)))
+     (list r-annotate
+           r-annotationdbi
+           r-annotationforge
+           r-biobase
+           r-category
+           r-go-db
+           r-graph
+           r-rgraphviz
+           r-rbgl))
     (home-page "https://bioconductor.org/packages/GOstats")
     (synopsis "Tools for manipulating GO and microarrays")
     (description
@@ -3227,25 +3447,25 @@ testing and other simple calculations.")
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "0946kkykms79mqnx262q20xzrrhv7cv723xh378335ff41qyf63n"))))
+         "1i8rryvagxk2pd8nl4a6yldwv82yx869nvv95jf8v00bna08f4d6"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-graph" ,r-graph)
-       ("r-xml" ,r-xml)))
+     (list r-annotate
+           r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-graph
+           r-xml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/GSEABase")
     (synopsis "Gene set enrichment data structures and methods")
     (description
@@ -3256,17 +3476,17 @@ Enrichment Analysis} (GSEA).")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "0q5pp04rq2gsh1kibvp8bvjkqc1kb46qpnj6agqp2vyqhrrfrm99"))))
+         "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76"))))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/hpar/")
     (synopsis "Human Protein Atlas in R")
     (description "This package provides a simple interface to and data from
@@ -3276,26 +3496,24 @@ the Human Protein Atlas project.")
 (define-public r-rhtslib
   (package
     (name "r-rhtslib")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhtslib" version))
        (sha256
         (base32
-         "0acpgv98529ic2i2k03knz05akb6h51wbz7sr5zgi8gk4nmawrlf"))))
+         "0pwmzwjf6agfp3bq6w8s3piwmzwjdd474qd8zmbzrm772qbadfr4"))))
     (properties `((upstream-name . "Rhtslib")))
     (build-system r-build-system)
     ;; Without this a temporary directory ends up in the Rhtslib.so binary,
     ;; which makes R abort the build.
     (arguments '(#:configure-flags '("--no-staged-install")))
     (propagated-inputs
-     `(("curl" ,curl)
-       ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list curl zlib ; packages using rhtslib need to link with zlib
+           r-zlibbioc))
     (native-inputs
-     `(("pkg-config" ,pkg-config)
-       ("r-knitr" ,r-knitr)))
+     (list pkg-config r-knitr))
     (home-page "https://github.com/nhayden/Rhtslib")
     (synopsis "High-throughput sequencing library as an R package")
     (description
@@ -3307,15 +3525,15 @@ of other R packages who wish to make use of HTSlib.")
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.66.0")
+    (version "1.68.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "0pprkv25avxhllddcssvqvy3nibmqkfwaq4xnlhka7858gyiyd1k"))))
+                "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5"))))
     (native-inputs
-     `(("gfortran" ,gfortran)))
+     (list gfortran))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/impute")
     (synopsis "Imputation for microarray data")
@@ -3327,23 +3545,21 @@ microarray data, using nearest neighbor averaging.")
 (define-public r-interactivedisplaybase
   (package
     (name "r-interactivedisplaybase")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "interactiveDisplayBase" version))
        (sha256
         (base32
-         "00rgrrmglslgb6j7whp0m5dlyl4436r647br05rrpv8cxrmbs2iv"))))
+         "1pi887192k1jifb4k3pf2jn5hcl1xmmy6vwl22r9njsprdyb3kab"))))
     (properties
      `((upstream-name . "interactiveDisplayBase")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-dt" ,r-dt)
-       ("r-shiny" ,r-shiny)))
+     (list r-biocgenerics r-dt r-shiny))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
     (synopsis "Base package for web displays of Bioconductor objects")
     (description
@@ -3354,22 +3570,20 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd"))))
+         "1np3i1k7rki9akh70156ggmid52yy0is9q5vd3s45ra7an0ap279"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-httr" ,r-httr)
-       ("r-png" ,r-png)))
+     (list r-biostrings r-httr r-png))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/KEGGREST")
     (synopsis "Client-side REST access to KEGG")
     (description
@@ -3380,13 +3594,13 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.48.3")
+    (version "3.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "0385ac0hvvml99krcgcpp6q7layjhzgp9xcxkcjrpfg5mjg1z4sx"))))
+                "05ypmax1s6y1nz42bxn61wxhzzw6185q633crzpdcbbz3dz4vgvy"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -3399,37 +3613,37 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "147nag4rz2xpjkkf8rmhja9k4ixjj1hsb0lq3lw7mw6q67zxsvf3"))))
+                "02px46h2ynprss7kwll3i0jz0clrdg0bys70jacd432xw34nm2sx"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-emdbook" ,r-emdbook)
-       ("r-fastseg" ,r-fastseg)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gtools" ,r-gtools)
-       ("r-iranges" ,r-iranges)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-limma" ,r-limma)
-       ("r-mclust" ,r-mclust)
-       ("r-mgcv" ,r-mgcv)
-       ("r-qvalue" ,r-qvalue)
-       ("r-r-utils" ,r-r-utils)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list r-data-table
+           r-emdbook
+           r-fastseg
+           r-genomeinfodb
+           r-genomicranges
+           r-gtools
+           r-iranges
+           r-kernsmooth
+           r-limma
+           r-mclust
+           r-mgcv
+           r-qvalue
+           r-r-utils
+           r-rcpp
+           r-rhtslib
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-zlibbioc))
     (native-inputs
-     `(("r-knitr" ,r-knitr))) ; for vignettes
+     (list r-knitr)) ; for vignettes
     (home-page "https://github.com/al2na/methylKit")
     (synopsis
      "DNA methylation analysis from high-throughput bisulfite sequencing results")
@@ -3457,12 +3671,12 @@ TAB-Seq.")
     (properties `((upstream-name . "motifRG")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-iranges" ,r-iranges)
-       ("r-seqlogo" ,r-seqlogo)
-       ("r-xvector" ,r-xvector)))
+     (list r-biostrings
+           r-bsgenome
+           r-bsgenome-hsapiens-ucsc-hg19
+           r-iranges
+           r-seqlogo
+           r-xvector))
     (home-page "https://bioconductor.org/packages/motifRG")
     (synopsis "Discover motifs in high throughput sequencing data")
     (description
@@ -3473,41 +3687,42 @@ throughput genetic sequencing data sets using regression methods.")
 (define-public r-mutationalpatterns
   (package
     (name "r-mutationalpatterns")
-    (version "3.2.0")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MutationalPatterns" version))
        (sha256
         (base32
-         "0433i4xbz8hrfaj8fxgzps3x8dqrl5vgwzg7qmp4cy5sb1lw5wvs"))))
+         "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl"))))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ;; These two packages are suggested packages
-       ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-cowplot" ,r-cowplot)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggalluvial" ,r-ggalluvial)
-       ("r-ggdendro" ,r-ggdendro)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-magrittr" ,r-magrittr)
-       ("r-nmf" ,r-nmf)
-       ("r-pracma" ,r-pracma)
-       ("r-purrr" ,r-purrr)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-biocgenerics
+           r-biostrings
+           r-bsgenome
+           ;; These two packages are suggested packages
+           r-bsgenome-hsapiens-1000genomes-hs37d5
+           r-bsgenome-hsapiens-ucsc-hg19
+           r-cowplot
+           r-dplyr
+           r-genomeinfodb
+           r-genomicranges
+           r-ggalluvial
+           r-ggdendro
+           r-ggplot2
+           r-iranges
+           r-magrittr
+           r-nmf
+           r-pracma
+           r-purrr
+           r-rcolorbrewer
+           r-s4vectors
+           r-stringr
+           r-tibble
+           r-tidyr
+           r-variantannotation))
     (home-page "https://bioconductor.org/packages/MutationalPatterns/")
     (synopsis "Extract and visualize mutational patterns in genomic data")
     (description "This package provides an extensive toolset for the
@@ -3518,41 +3733,41 @@ in SNV base substitution data.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.18.0")
+    (version "2.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "1z7s17j6zgb70m0khyf9icqlnbnzlivca7vw7j0vxyw417ld9lkr"))))
+         "0ip614mdwisz2hlmyfgngysq1s3hajb88cgdmygfc8i6kyxjkjzl"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-digest" ,r-digest)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-impute" ,r-impute)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-maldiquant" ,r-maldiquant)
-       ("r-mass" ,r-mass)
-       ("r-mscoreutils" ,r-mscoreutils)
-       ("r-mzid" ,r-mzid)
-       ("r-mzr" ,r-mzr)
-       ("r-pcamethods" ,r-pcamethods)
-       ("r-plyr" ,r-plyr)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rcpp" ,r-rcpp)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-vsn" ,r-vsn)
-       ("r-xml" ,r-xml)))
+     (list r-affy
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-digest
+           r-ggplot2
+           r-impute
+           r-iranges
+           r-lattice
+           r-maldiquant
+           r-mass
+           r-mscoreutils
+           r-mzid
+           r-mzr
+           r-pcamethods
+           r-plyr
+           r-protgenerics
+           r-rcpp
+           r-s4vectors
+           r-scales
+           r-vsn
+           r-xml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/lgatto/MSnbase")
     (synopsis "Base functions and classes for MS-based proteomics")
     (description
@@ -3563,14 +3778,14 @@ of mass spectrometry based proteomics data.")
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "0r3vgigf4fk0xzfg8gcvad01jdh0fysh6x22m9qy77x6glyrxcj2"))))
+         "0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (arguments
@@ -3579,32 +3794,32 @@ of mass spectrometry based proteomics data.")
          (add-after 'unpack 'set-HOME
            (lambda _ (setenv "HOME" "/tmp"))))))
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationhub" ,r-annotationhub)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocstyle" ,r-biocstyle)
-       ("r-biostrings" ,r-biostrings)
-       ("r-data-table" ,r-data-table)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dplyr" ,r-dplyr)
-       ("r-foreach" ,r-foreach)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iterators" ,r-iterators)
-       ("r-msnbase" ,r-msnbase)
-       ("r-msmstests" ,r-msmstests)
-       ("r-mzid" ,r-mzid)
-       ("r-mzr" ,r-mzr)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-purrr" ,r-purrr)
-       ("r-r-cache" ,r-r-cache)
-       ("r-rcpp" ,r-rcpp)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rlang" ,r-rlang)
-       ("r-runit" ,r-runit)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-xtable" ,r-xtable)))
+     (list r-annotationdbi
+           r-annotationhub
+           r-biobase
+           r-biocgenerics
+           r-biocstyle
+           r-biostrings
+           r-data-table
+           r-doparallel
+           r-dplyr
+           r-foreach
+           r-ggplot2
+           r-iterators
+           r-msnbase
+           r-msmstests
+           r-mzid
+           r-mzr
+           r-protgenerics
+           r-purrr
+           r-r-cache
+           r-rcpp
+           r-reshape2
+           r-rlang
+           r-runit
+           r-stringr
+           r-tibble
+           r-xtable))
     (home-page "https://bioconductor.org/packages/MSnID")
     (synopsis "Utilities for LC-MSn proteomics identifications")
     (description
@@ -3620,25 +3835,25 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-mzid
   (package
     (name "r-mzid")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzID" version))
        (sha256
         (base32
-         "1wsy6frxa5602jqb1nlqv39mzgpid8wfyvb9m2jb6srv7p59rgys"))))
+         "0r001amd4m99cv0ixw38rpz0zv0xqb0qyvs16bz1i4a756391qri"))))
     (properties `((upstream-name . "mzID")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-doparallel" ,r-doparallel)
-       ("r-foreach" ,r-foreach)
-       ("r-iterators" ,r-iterators)
-       ("r-plyr" ,r-plyr)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-xml" ,r-xml)))
+     (list r-doparallel
+           r-foreach
+           r-iterators
+           r-plyr
+           r-protgenerics
+           r-xml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/mzID")
     (synopsis "Parser for mzIdentML files")
     (description
@@ -3651,14 +3866,14 @@ specific parser.")
 (define-public r-mzr
   (package
     (name "r-mzr")
-    (version "2.26.1")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzR" version))
        (sha256
         (base32
-         "0z4cz6lir9gwzy0hxwv03wv36fkkfdb97p9wv4af020k0zkp3ipr"))
+         "1azq0wjjy6n5xc721gjz6afm43ajz15b4p34vgsdjzwg9qn1vrs1"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -3680,20 +3895,20 @@ specific parser.")
 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
              #t)))))
     (inputs
-     `(;; Our default boost package won't work here, unfortunately, even with
-       ;; mzR version 2.26.1.
-       ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
-       ("zlib" ,zlib)))
+     (list ;; Our default boost package won't work here, unfortunately, even with
+           ;; mzR version 2.28.0.
+           boost-for-mysql ; use this instead of the bundled boost sources
+           zlib))
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-ncdf4" ,r-ncdf4)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list r-biobase
+           r-biocgenerics
+           r-ncdf4
+           r-protgenerics
+           r-rcpp
+           r-rhdf5lib
+           r-zlibbioc))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/sneumann/mzR/")
     (synopsis "Parser for mass spectrometry data files")
     (description
@@ -3708,28 +3923,28 @@ previously been used in XCMS.")
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OrganismDbi" version))
        (sha256
         (base32
-         "0p8ccpdchdwci4kv9y07wdadzgms8nipvg6rm1rll35jcflnnkxi"))))
+         "0zp6x2iqhn9s3xp07yilnr6hn73acvkdai5xip4iiwjdlnfffj83"))))
     (properties `((upstream-name . "OrganismDbi")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-dbi" ,r-dbi)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-graph" ,r-graph)
-       ("r-iranges" ,r-iranges)
-       ("r-rbgl" ,r-rbgl)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-biocmanager
+           r-dbi
+           r-genomicfeatures
+           r-genomicranges
+           r-graph
+           r-iranges
+           r-rbgl
+           r-s4vectors))
     (home-page "https://bioconductor.org/packages/OrganismDbi")
     (synopsis "Software to enable the smooth interfacing of database packages")
     (description "The package enables a simple unified interface to several
@@ -3740,21 +3955,18 @@ the fact that each of these packages implements a select methods.")
 (define-public r-pcamethods
   (package
     (name "r-pcamethods")
-    (version "1.84.0")
+    (version "1.86.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pcaMethods" version))
        (sha256
         (base32
-         "1ccqsxn487dy92c2d1iffh9917z4zq5ia92zv2h6pi00jjc6ymb5"))))
+         "1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg"))))
     (properties `((upstream-name . "pcaMethods")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-mass" ,r-mass)
-       ("r-rcpp" ,r-rcpp)))
+     (list r-biobase r-biocgenerics r-mass r-rcpp))
     (home-page "https://github.com/hredestig/pcamethods")
     (synopsis "Collection of PCA methods")
     (description
@@ -3770,14 +3982,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ProtGenerics" version))
        (sha256
         (base32
-         "1c79k8nc28782w5gxi7pkm8jmddq1hdw6khs9kgsp8dyk60ak6fq"))))
+         "0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0"))))
     (properties `((upstream-name . "ProtGenerics")))
     (build-system r-build-system)
     (home-page "https://github.com/lgatto/ProtGenerics")
@@ -3790,19 +4002,18 @@ proteomics packages.")
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "0l40ibf8g5s4ay83s92l198jjqc5l09hcmxqcjrpifvp5pjf9yy5"))))
+         "0k2p1lwdvix4n742a97lv988rx5kg8cvcmzgyzj0538n1nz0lxk0"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bh" ,r-bh)
-       ("r-graph" ,r-graph)))
+     (list r-bh r-graph))
     (home-page "https://www.bioconductor.org/packages/RBGL")
     (synopsis "Interface to the Boost graph library")
     (description
@@ -3813,45 +4024,45 @@ the graph algorithms contained in the Boost library.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "0l92v870ndna8zjqwzf22fb9vyhkh6942v4gaiqr1yc4qr521p5p"))))
+                "02zwz7c8ljmdcfxj54xns0a31sj616x63q63wxhxa1nb4dhgmvk7"))))
     (properties `((upstream-name . "RCAS")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-cowplot" ,r-cowplot)
-       ("r-data-table" ,r-data-table)
-       ("r-dt" ,r-dt)
-       ("r-genomation" ,r-genomation)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggseqlogo" ,r-ggseqlogo)
-       ("r-gprofiler2" ,r-gprofiler2)
-       ("r-iranges" ,r-iranges)
-       ("r-knitr" ,r-knitr)
-       ("r-pbapply" ,r-pbapply)
-       ("r-pheatmap" ,r-pheatmap)
-       ("r-plotly" ,r-plotly)
-       ("r-plotrix" ,r-plotrix)
-       ("r-proxy" ,r-proxy)
-       ("r-ranger" ,r-ranger)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("r-s4vectors" ,r-s4vectors)
-       ("pandoc" ,pandoc)))
+     (list r-biocgenerics
+           r-biostrings
+           r-bsgenome
+           r-bsgenome-hsapiens-ucsc-hg19
+           r-cowplot
+           r-data-table
+           r-dt
+           r-genomation
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-ggseqlogo
+           r-gprofiler2
+           r-iranges
+           r-knitr
+           r-pbapply
+           r-pheatmap
+           r-plotly
+           r-plotrix
+           r-proxy
+           r-ranger
+           r-rsqlite
+           r-rtracklayer
+           r-rmarkdown
+           r-s4vectors
+           pandoc))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (synopsis "RNA-centric annotation system")
     (description
      "RCAS aims to be a standalone RNA-centric annotation system that provides
@@ -3863,27 +4074,27 @@ library implementing most of the pipeline's features.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl"))))
+         "0y1mawzfvxrympc47q3isk96sl9d1bc8kdsxpm8rnhqg5bmgwya6"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-memoise" ,r-memoise)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biostrings
+           r-bsgenome
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-memoise
+           r-rtracklayer
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/regioneR/")
     (synopsis "Association analysis of genomic regions")
     (description "This package offers a statistical framework based on
@@ -3894,39 +4105,39 @@ region sets and other genomic features.")
 (define-public r-reportingtools
   (package
     (name "r-reportingtools")
-    (version "2.32.1")
+    (version "2.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReportingTools" version))
        (sha256
         (base32
-         "0wq9y649dh1am6djzz0xlz42428xsgw2bdx1dknhdw2xbydmmx47"))))
+         "06kwf87h84xgswkrm7brmgr9aj1nf6cxp24hrfymkzq2pha5y5j7"))))
     (properties
      `((upstream-name . "ReportingTools")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-category" ,r-category)
-       ("r-deseq2" ,r-deseq2)
-       ("r-edger" ,r-edger)
-       ("r-ggbio" ,r-ggbio)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gostats" ,r-gostats)
-       ("r-gseabase" ,r-gseabase)
-       ("r-hwriter" ,r-hwriter)
-       ("r-iranges" ,r-iranges)
-       ("r-knitr" ,r-knitr)
-       ("r-lattice" ,r-lattice)
-       ("r-limma" ,r-limma)
-       ("r-pfam-db" ,r-pfam-db)
-       ("r-r-utils" ,r-r-utils)
-       ("r-xml" ,r-xml)))
+     (list r-annotate
+           r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-category
+           r-deseq2
+           r-edger
+           r-ggbio
+           r-ggplot2
+           r-gostats
+           r-gseabase
+           r-hwriter
+           r-iranges
+           r-knitr
+           r-lattice
+           r-limma
+           r-pfam-db
+           r-r-utils
+           r-xml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/ReportingTools/")
     (synopsis "Tools for making reports in various formats")
     (description
@@ -3944,19 +4155,18 @@ browser.")
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.36.0")
+    (version "2.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "1a5kw9ry9cr258al0x3q0ss5xn1ymscdypx51vzzgzamhy7dqakz"))))
+                "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-rhdf5filters" ,r-rhdf5filters)
-       ("r-rhdf5lib" ,r-rhdf5lib)))
+     (list r-rhdf5filters r-rhdf5lib))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/rhdf5")
     (synopsis "HDF5 interface to R")
     (description
@@ -3972,22 +4182,22 @@ the available RAM.")
 (define-public r-rhdf5filters
   (package
     (name "r-rhdf5filters")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rhdf5filters" version))
        (sha256
         (base32
-         "133v0s452acspi4dbf6gsa2xrr0qza86jdjjbpwhdv6zfd1djbgc"))))
+         "05b015pyp3g1crmm2d3ldsa7r5w0khmf87qbl4fv16r6pdggha78"))))
     (properties `((upstream-name . "rhdf5filters")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-rhdf5lib" ,r-rhdf5lib)))
+     (list r-rhdf5lib))
     (inputs
-     `(("zlib" ,zlib)))
+     (list zlib))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/grimbough/rhdf5filters")
     (synopsis "HDF5 compression filters")
     (description
@@ -3998,13 +4208,13 @@ HDF5 datasets.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.8.0")
+    (version "2.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0arhh5bbx3pmxmkh5sjgczcswqy83d35r7cjhd2knpczdvrixaq5"))))
+                "0v6b3j45ivd9f04fpfs1vjwby5pi30mf5683bjxim01vi2krj9yh"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -4018,16 +4228,16 @@ HDF5 datasets.")
              (substitute* "NAMESPACE"
                (("import\\(zlibbioc\\)") "")))))))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bitops" ,r-bitops)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
+     (list r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-bitops
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-rhtslib
+           r-s4vectors
+           r-xvector))
     (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
     (synopsis "Interface to samtools, bcftools, and tabix")
     (description
@@ -4053,11 +4263,7 @@ tab-delimited (tabix) files.")
     (properties `((upstream-name . "restfulr")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-rcurl" ,r-rcurl)
-       ("r-rjson" ,r-rjson)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xml" ,r-xml)
-       ("r-yaml" ,r-yaml)))
+     (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
     (home-page "https://cran.r-project.org/package=restfulr")
     (synopsis "R interface to RESTful web services")
     (description
@@ -4067,13 +4273,13 @@ tab-delimited (tabix) files.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.52.1")
+    (version "1.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "11w6dx09pb49lin1gr9q88xn7ixh9jd5z6m9z27djchm0nw10lx9"))))
+                "11bh9khra2qdmicppi6ya43kf8f1z13ak92vkl6nr5f20k54cphc"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -4085,24 +4291,24 @@ tab-delimited (tabix) files.")
              (substitute* "NAMESPACE"
                (("import\\(zlibbioc\\)") "")))))))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     (list pkg-config))
     (inputs
-     `(("zlib" ,zlib)))
+     (list zlib))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocio" ,r-biocio)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rcurl" ,r-rcurl)
-       ("r-restfulr" ,r-restfulr)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xml" ,r-xml)
-       ("r-xvector" ,r-xvector)
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list r-biocgenerics
+           r-biocio
+           r-biostrings
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-iranges
+           r-rcurl
+           r-restfulr
+           r-rsamtools
+           r-s4vectors
+           r-xml
+           r-xvector
+           r-zlibbioc))
     (home-page "https://bioconductor.org/packages/rtracklayer")
     (synopsis "R interface to genome browsers and their annotation tracks")
     (description
@@ -4128,13 +4334,13 @@ as well as query and modify the browser state, such as the current viewport.")
     (properties `((upstream-name . "samr")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-gsa" ,r-gsa)
-       ("r-impute" ,r-impute)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-openxlsx" ,r-openxlsx)
-       ("r-shiny" ,r-shiny)
-       ("r-shinyfiles" ,r-shinyfiles)))
-    (native-inputs `(("gfortran" ,gfortran)))
+     (list r-gsa
+           r-impute
+           r-matrixstats
+           r-openxlsx
+           r-shiny
+           r-shinyfiles))
+    (native-inputs (list gfortran))
     (home-page "https://statweb.stanford.edu/~tibs/SAM/")
     (synopsis "Significance analysis of Microarrays")
     (description
@@ -4143,21 +4349,61 @@ differential expression analysis, RNAseq data and related problems.")
     ;; Any version of the LGPL
     (license license:lgpl3+)))
 
+(define-public r-scdblfinder
+  (package
+    (name "r-scdblfinder")
+    (version "1.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scDblFinder" version))
+       (sha256
+        (base32 "0wzmmcsnjybgzbc5rn4i72n26j9n59dfy1zg8ij0q8p4276jplsd"))))
+    (properties `((upstream-name . "scDblFinder")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biocneighbors
+           r-biocparallel
+           r-biocsingular
+           r-bluster
+           r-delayedarray
+           r-igraph
+           r-mass
+           r-matrix
+           r-s4vectors
+           r-scater
+           r-scran
+           r-scuttle
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/plger/scDblFinder")
+    (synopsis "Detect multiplets in single-cell RNA sequencing data")
+    (description
+     "The scDblFinder package gathers various methods for the detection and
+handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
+multiple cells captured within the same droplet or reaction volume).  It
+includes methods formerly found in the scran package, and the new fast and
+comprehensive scDblFinder method.")
+    (license license:gpl3)))
+
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqLogo" version))
        (sha256
         (base32
-         "1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp"))))
+         "013hwj2lp29nqa8mkvm25aliarg0k725crg4cpsbj0iiskyrs6rl"))))
     (properties `((upstream-name . "seqLogo")))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/seqLogo")
     (synopsis "Sequence logos for DNA sequence alignments")
     (description
@@ -4169,22 +4415,18 @@ Stephens (1990).")
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "seqPattern" version))
               (sha256
                (base32
-                "0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay"))))
+                "1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na"))))
     (properties
      `((upstream-name . "seqPattern")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-plotrix" ,r-plotrix)))
+     (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
     (home-page "https://bioconductor.org/packages/seqPattern")
     (synopsis "Visualising oligonucleotide patterns and motif occurrences")
     (description
@@ -4196,35 +4438,35 @@ reference point and sorted by a user defined feature.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "0zqinw3c6h5v1c5nhzkiziirws16nbviccgw8nj2d22r33dbqwp3"))))
+         "1p17v15wd3v6w9ligpjjk28vy8k2ql57y2hhm8y6vnv9y3nagjsx"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
-     `(("zlib" ,zlib)))
+     (list zlib))
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-hwriter" ,r-hwriter)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-latticeextra" ,r-latticeextra)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-rhtslib
+           r-hwriter
+           r-iranges
+           r-lattice
+           r-latticeextra
+           r-rsamtools
+           r-s4vectors
+           r-xvector
+           r-zlibbioc))
     (home-page "https://bioconductor.org/packages/ShortRead")
     (synopsis "FASTQ input and manipulation tools")
     (description
@@ -4239,34 +4481,34 @@ ungapped alignment formats.")
 (define-public r-simplifyenrichment
   (package
     (name "r-simplifyenrichment")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "simplifyEnrichment" version))
        (sha256
         (base32
-         "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh"))))
+         "05d9yjd8s7q1q78qmnx5xfrz9ppswc2cpfmjj47d338w783lwk98"))))
     (properties
      `((upstream-name . "simplifyEnrichment")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-circlize" ,r-circlize)
-       ("r-clue" ,r-clue)
-       ("r-cluster" ,r-cluster)
-       ("r-complexheatmap" ,r-complexheatmap)
-       ("r-digest" ,r-digest)
-       ("r-getoptlong" ,r-getoptlong)
-       ("r-go-db" ,r-go-db)
-       ("r-gosemsim" ,r-gosemsim)
-       ("r-matrix" ,r-matrix)
-       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
-       ("r-proxyc" ,r-proxyc)
-       ("r-slam" ,r-slam)
-       ("r-tm" ,r-tm)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-annotationdbi
+           r-biocgenerics
+           r-circlize
+           r-clue
+           r-cluster
+           r-complexheatmap
+           r-digest
+           r-getoptlong
+           r-go-db
+           r-gosemsim
+           r-matrix
+           r-org-hs-eg-db
+           r-proxyc
+           r-slam
+           r-tm))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/jokergoo/simplifyEnrichment")
     (synopsis "Simplify functional enrichment results")
     (description "This package provides a new clustering algorithm, binary
@@ -4275,27 +4517,74 @@ this package.  It also provides functionalities for visualizing, summarizing
 and comparing the clusterings.")
     (license license:expat)))
 
+(define-public r-transcriptr
+  (package
+    (name "r-transcriptr")
+    (version "1.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "transcriptR" version))
+       (sha256
+        (base32 "1p5l2z3szx3qh02x7r81ajl7yc5wqsri6q6pzw83livmalcli5yy"))))
+    (properties `((upstream-name . "transcriptR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-caret
+           r-chipseq
+           r-e1071
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-proc
+           r-reshape2
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/transcriptR")
+    (synopsis "Primary transcripts detection and quantification")
+    (description
+     "The differences in the RNA types being sequenced have an impact on the
+resulting sequencing profiles.  mRNA-seq data is enriched with reads derived
+from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
+broader coverage of both exonic and intronic regions.  The presence of
+intronic reads in GRO-seq type of data makes it possible to use it to
+computationally identify and quantify all de novo continuous regions of
+transcription distributed across the genome.  This type of data, however, is
+more challenging to interpret and less common practice compared to mRNA-seq.
+One of the challenges for primary transcript detection concerns the
+simultaneous transcription of closely spaced genes, which needs to be properly
+divided into individually transcribed units.  The R package transcriptR
+combines RNA-seq data with ChIP-seq data of histone modifications that mark
+active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
+overcome this challenge.  The advantage of this approach over the use of, for
+example, gene annotations is that this approach is data driven and therefore
+able to deal also with novel and case specific events.")
+    (license license:gpl3)))
+
 (define-public r-trajectoryutils
   (package
     (name "r-trajectoryutils")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TrajectoryUtils" version))
        (sha256
         (base32
-         "1b7mg3ypp1ay98cav47h9vn692lx0n9b5b0hpansgnkr5prb823b"))))
+         "0pzm1h69bg04a2v09r8c6pb3pix6f3n5dylvbv7wsp574qfaqyd1"))))
     (properties
      `((upstream-name . "TrajectoryUtils")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-igraph" ,r-igraph)
-       ("r-matrix" ,r-matrix)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/TrajectoryUtils")
     (synopsis "Single-cell trajectory analysis utilities")
     (description
@@ -4308,24 +4597,24 @@ structures to hold pseudotime inference results.")
 (define-public r-slingshot
   (package
    (name "r-slingshot")
-   (version "2.0.0")
+   (version "2.2.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "slingshot" version))
             (sha256
              (base32
-              "1aqsz2kxwax8d8d5iv3zk5hlyk5aya1wbxs1wky2rgccw4d35whx"))))
+              "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa"))))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-igraph" ,r-igraph)
-      ("r-matrixstats" ,r-matrixstats)
-      ("r-princurve" ,r-princurve)
-      ("r-s4vectors" ,r-s4vectors)
-      ("r-singlecellexperiment" ,r-singlecellexperiment)
-      ("r-summarizedexperiment" ,r-summarizedexperiment)
-      ("r-trajectoryutils" ,r-trajectoryutils)))
+    (list r-igraph
+          r-matrixstats
+          r-princurve
+          r-s4vectors
+          r-singlecellexperiment
+          r-summarizedexperiment
+          r-trajectoryutils))
    (native-inputs
-    `(("r-knitr" ,r-knitr)))
+    (list r-knitr))
    (home-page "https://bioconductor.org/packages/slingshot")
    (synopsis "Tools for ordering single-cell sequencing")
    (description "This package provides functions for inferring continuous,
@@ -4337,34 +4626,67 @@ events and allows for the incorporation of prior knowledge through supervised
 graph construction.")
    (license license:artistic2.0)))
 
+(define-public r-stringdb
+  (package
+    (name "r-stringdb")
+    (version "2.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "STRINGdb" version))
+       (sha256
+        (base32 "1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm"))))
+    (properties `((upstream-name . "STRINGdb")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-gplots
+           r-hash
+           r-igraph
+           r-plotrix
+           r-plyr
+           r-png
+           r-rcolorbrewer
+           r-rcurl
+           r-sqldf))
+    (home-page "https://git.bioconductor.org/packages/STRINGdb")
+    (synopsis "Search tool for the retrieval of interacting proteins database")
+    (description
+     "The @code{STRINGdb} package provides an R interface to the STRING
+protein-protein interactions database.  @url{https://www.string-db.org,
+STRING} is a database of known and predicted protein-protein interactions.
+The interactions include direct (physical) and indirect (functional)
+associations.  Each interaction is associated with a combined confidence score
+that integrates the various evidences.")
+    (license license:gpl2)))
+
 (define-public r-structuralvariantannotation
   (package
     (name "r-structuralvariantannotation")
-    (version "1.8.2")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "StructuralVariantAnnotation" version))
        (sha256
-        (base32 "04ac4mjh3pgdlws0aiacqg0vd7bhg890w44r7b90p947c3rk1mfw"))))
+        (base32 "009l27kb9gvwwf57dwxfribhfhvn4z5pw8yc847l6pkbzqggx678"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-assertthat" ,r-assertthat)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rlang" ,r-rlang)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-stringr" ,r-stringr)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-assertthat
+           r-biocgenerics
+           r-biostrings
+           r-dplyr
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-rlang
+           r-rtracklayer
+           r-s4vectors
+           r-stringr
+           r-summarizedexperiment
+           r-variantannotation))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
     (synopsis "R package designed to simplify structural variant analysis")
     (description
@@ -4377,28 +4699,28 @@ involving two separate genomic loci encoded as GRanges objects.")
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g"))))
+                "0qpnx2aii9vs7fcp0ax5j77ysbhi4qhjhm35vnygs3isbrjn925a"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixgenerics" ,r-matrixgenerics)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biobase
+           r-biocgenerics
+           r-delayedarray
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-matrix
+           r-matrixgenerics
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/SummarizedExperiment")
     (synopsis "Container for representing genomic ranges by sample")
     (description
@@ -4411,22 +4733,22 @@ samples.")
 (define-public r-sva
   (package
     (name "r-sva")
-    (version "3.40.0")
+    (version "3.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sva" version))
        (sha256
         (base32
-         "12jkcybdfspabh7x124d44l9fj1hwwg3gvcqxvz5wpkiflc2vkji"))))
+         "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-edger" ,r-edger)
-       ("r-genefilter" ,r-genefilter)
-       ("r-mgcv" ,r-mgcv)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-limma" ,r-limma)))
+     (list r-edger
+           r-genefilter
+           r-mgcv
+           r-biocparallel
+           r-matrixstats
+           r-limma))
     (home-page "https://bioconductor.org/packages/sva")
     (synopsis "Surrogate variable analysis")
     (description
@@ -4442,46 +4764,32 @@ unmodeled, or latent sources of noise.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "1.26.3")
+    (version "2.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "01l35l5zj87qkarrbal9la6kshk3j7k8hy3iimv3gdnnz4axmvs7"))))
+         "1j91pyfjsqngxxlxjqc477pznlfax4vayrks2q12rxw76ija80hf"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-assertthat" ,r-assertthat)
-       ("r-batchtools" ,r-batchtools)
-       ("r-biostrings" ,r-biostrings)
-       ("r-crayon" ,r-crayon)
-       ("r-deseq2" ,r-deseq2)
-       ("r-dot" ,r-dot)
-       ("r-edger" ,r-edger)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-go-db" ,r-go-db)
-       ("r-gostats" ,r-gostats)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-magrittr" ,r-magrittr)
-       ("r-pheatmap" ,r-pheatmap)
-       ("r-rjson" ,r-rjson)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rsvg" ,r-rsvg)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shortread" ,r-shortread)
-       ("r-stringr" ,r-stringr)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-testthat" ,r-testthat)
-       ("r-yaml" ,r-yaml)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-biocgenerics
+           r-biostrings
+           r-crayon
+           r-genomicranges
+           r-ggplot2
+           r-htmlwidgets
+           r-magrittr
+           r-rsamtools
+           r-s4vectors
+           r-shortread
+           r-stringr
+           r-summarizedexperiment
+           r-yaml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/tgirke/systemPipeR")
     (synopsis "Next generation sequencing workflow and reporting environment")
     (description
@@ -4499,26 +4807,26 @@ annotation infrastructure.")
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.44.0")
+    (version "2.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "1ggi7yrhkyi85p3sfj3yd95n9mzq1xpff28ixa4dl9yzasks1v5a"))))
+                "01vykf8bzwm2k7cfj09r6il6qaycjy10wpaxbn13f21p66r5nlm2"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-dbi" ,r-dbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-go-db" ,r-go-db)
-       ("r-graph" ,r-graph)
-       ("r-lattice" ,r-lattice)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-sparsem" ,r-sparsem)))
+     (list r-annotationdbi
+           r-dbi
+           r-biobase
+           r-biocgenerics
+           r-go-db
+           r-graph
+           r-lattice
+           r-matrixstats
+           r-sparsem))
     (home-page "https://bioconductor.org/packages/topGO")
     (synopsis "Enrichment analysis for gene ontology")
     (description
@@ -4532,16 +4840,16 @@ dependencies between GO terms can be implemented and applied.")
 (define-public r-tximport
   (package
     (name "r-tximport")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tximport" version))
               (sha256
                (base32
-                "0ip2yr0zspf2aagskxl4dwncr48dw5qb90an3sswnnh2dqdb82if"))))
+                "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4"))))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/tximport")
     (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
     (description
@@ -4553,37 +4861,70 @@ provided as a matrix which can be used as an offset for different expression
 of gene-level counts.")
     (license license:gpl2+)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-valr
+  (package
+    (name "r-valr")
+    (version "0.6.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "valr" version))
+       (sha256
+        (base32
+         "0dd41irvibh6rwi52bw4zg4m7wpyihlp1kdkb8fdji3csw2fiz4k"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-broom
+           r-dplyr
+           r-ggplot2
+           r-rcpp
+           r-readr
+           r-rlang
+           r-rtracklayer ;bioconductor package
+           r-stringr
+           r-tibble))
+    (native-inputs
+     (list r-knitr))
+    (home-page "https://github.com/rnabioco/valr")
+    (synopsis "Genome interval arithmetic in R")
+    (description
+     "This package enables you to read and manipulate genome intervals and
+signals.  It provides functionality similar to command-line tool suites within
+R, enabling interactive analysis and visualization of genome-scale data.")
+    (license license:expat)))
+
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.38.0")
+    (version "1.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "0c9r00j8a3bs6n0dv4wi17jc1ljzvr3r2bi4h9axhcsf2ip906rh"))))
+                "1r9kayp0hxcwls08lv2fh0cmf9ks0lqx3k31c1zn4asw4dyqpgva"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixgenerics" ,r-matrixgenerics)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-biostrings
+           r-bsgenome
+           r-dbi
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-matrixgenerics
+           r-summarizedexperiment
+           r-rhtslib
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-xvector
+           r-zlibbioc))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/VariantAnnotation")
     (synopsis "Package for annotation of genetic variants")
@@ -4594,23 +4935,19 @@ coding changes and predict coding outcomes.")
 (define-public r-vsn
   (package
     (name "r-vsn")
-    (version "3.60.0")
+    (version "3.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "vsn" version))
        (sha256
         (base32
-         "0nppph3kv8z83368snb8s3n4vcqj829yyi1kh4q09qvq18rhvssv"))))
+         "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-biobase" ,r-biobase)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-lattice" ,r-lattice)
-       ("r-limma" ,r-limma)))
+     (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
     (native-inputs
-     `(("r-knitr" ,r-knitr))) ; for vignettes
+     (list r-knitr)) ; for vignettes
     (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
     (synopsis "Variance stabilization and calibration for microarray data")
     (description
@@ -4627,16 +4964,79 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
+(define-public r-xina
+  (package
+    (name "r-xina")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "XINA" version))
+       (sha256
+        (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp"))))
+    (properties `((upstream-name . "XINA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-alluvial
+           r-ggplot2
+           r-gridextra
+           r-igraph
+           r-mclust
+           r-plyr
+           r-stringdb))
+    (native-inputs (list r-knitr))
+    (home-page "https://git.bioconductor.org/packages/XINA")
+    (synopsis "Identifying proteins that exhibit similar patterns")
+    (description
+     "The aim of @code{XINA} is to determine which proteins exhibit similar
+patterns within and across experimental conditions, since proteins with
+co-abundance patterns may have common molecular functions.  @code{XINA} imports
+multiple datasets, tags dataset in silico, and combines the data for subsequent
+subgrouping into multiple clusters.  The result is a single output depicting
+the variation across all conditions.  @code{XINA} not only extracts
+coabundance profiles within and across experiments, but also incorporates
+protein-protein interaction databases and integrative resources such as
+@dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
+molecular functions, respectively, and produces intuitive graphical outputs.")
+    (license license:gpl3)))
+
+(define-public r-xmapbridge
+  (package
+    (name "r-xmapbridge")
+    (version "1.52.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "xmapbridge" version))
+       (sha256
+        (base32 "1zsqhisbq6f9qgw9f0a6ixxh635h3qm17117yfns5nnfw73ndlgi"))))
+    (properties `((upstream-name . "xmapbridge")))
+    (build-system r-build-system)
+    (home-page "https://git.bioconductor.org/packages/xmapbridge")
+    (synopsis "Display numeric data in the web based genome browser X:MAP")
+    (description
+     "The package @code{xmapbridge} can plot graphs in the X:Map genome
+browser.  X:Map uses the Google Maps API to provide a scrollable view of the
+genome.  It supports a number of species, and can be accessed at
+@url{http://xmap.picr.man.ac.uk}.  This package exports plotting files in a
+suitable format.  Graph plotting in R is done using calls to the functions
+@code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
+similar to those used by the standard plot methods in R.  These result in data
+being written to a set of files (in a specific directory structure) that
+contain the data to be displayed, as well as some additional meta-data
+describing each of the graphs.")
+    (license license:lgpl3)))
+
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.32.0")
+    (version "0.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "1cw34gd9iaspl0v737xl7rngq63zrj03a5ngai15ggrnv1sq2aqr"))))
+                "07r4qgmnifw9jk2srjg0cvl310j0f9y35jrg0zqhlvhmyhg6n2c0"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
@@ -4651,11 +5051,9 @@ and specific in detecting differential transcription.")
                (("import\\(zlibbioc\\)") ""))
              #t)))))
     (inputs
-     `(("zlib" ,zlib)))
+     (list zlib))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocgenerics r-iranges r-s4vectors))
     (home-page "https://bioconductor.org/packages/XVector")
     (synopsis "Representation and manpulation of external sequences")
     (description
@@ -4666,13 +5064,13 @@ and specific in detecting differential transcription.")
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
-    (version "1.38.0")
+    (version "1.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "zlibbioc" version))
               (sha256
                (base32
-                "1dv5bf12kzk1yzyfs3g5syim16sbi44kalvzj2i2xcnxnl6x60ip"))))
+                "0a0dl7z58zxdj6938zbxixphgljj1giylk1nd05bb7qsccmp0xhj"))))
     (properties
      `((upstream-name . "zlibbioc")))
     (build-system r-build-system)
@@ -4682,25 +5080,57 @@ and specific in detecting differential transcription.")
 libraries for systems that do not have these available via other means.")
     (license license:artistic2.0)))
 
+(define-public r-zellkonverter
+  (package
+    (name "r-zellkonverter")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "zellkonverter" version))
+       (sha256
+        (base32 "1ihp2f23lpdfgf3qliy22vrq8czm353hyhqf74r5r712190k6pgg"))))
+    (properties `((upstream-name . "zellkonverter")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-basilisk
+           r-cli
+           r-delayedarray
+           r-matrix
+           r-reticulate
+           r-s4vectors
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/theislab/zellkonverter")
+    (synopsis "Conversion between AnnData and single-cell experiments objects")
+    (description
+     "This package provides methods to convert between Python AnnData objects
+and SingleCellExperiment objects.  These are primarily intended for use by
+downstream Bioconductor packages that wrap Python methods for single-cell data
+analysis.  It also includes functions to read and write H5AD files used for
+saving AnnData objects to disk.")
+    (license license:expat)))
+
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z"))))
+         "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-lattice" ,r-lattice)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+     (list r-annotate
+           r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-lattice
+           r-rcolorbrewer))
     (home-page "https://bioconductor.org/packages/geneplotter")
     (synopsis "Graphics functions for genomic data")
     (description
@@ -4710,30 +5140,30 @@ libraries for systems that do not have these available via other means.")
 (define-public r-oligoclasses
   (package
     (name "r-oligoclasses")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligoClasses" version))
        (sha256
         (base32
-         "1nsfyfpj264h6y322pzz0i001b0m862j3skbq5rjwlrj1p8j2gi7"))))
+         "1ia2f19swiwb0552nfwkai4gl0av07cj75b6jwiviqa1bli09264"))))
     (properties `((upstream-name . "oligoClasses")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affyio" ,r-affyio)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dbi" ,r-dbi)
-       ("r-ff" ,r-ff)
-       ("r-foreach" ,r-foreach)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-affyio
+           r-biobase
+           r-biocgenerics
+           r-biocmanager
+           r-biostrings
+           r-dbi
+           r-ff
+           r-foreach
+           r-genomicranges
+           r-iranges
+           r-rsqlite
+           r-s4vectors
+           r-summarizedexperiment))
     (home-page "https://bioconductor.org/packages/oligoClasses/")
     (synopsis "Classes for high-throughput arrays")
     (description
@@ -4745,31 +5175,31 @@ packages.")
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "0fyq77im6s79havjwbchhqhnllxs134jsi98g6msxz66h16lj3al"))))
+         "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
-    (inputs `(("zlib" ,zlib)))
+    (inputs (list zlib))
     (propagated-inputs
-     `(("r-affxparser" ,r-affxparser)
-       ("r-affyio" ,r-affyio)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dbi" ,r-dbi)
-       ("r-ff" ,r-ff)
-       ("r-oligoclasses" ,r-oligoclasses)
-       ("r-preprocesscore" ,r-preprocesscore)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list r-affxparser
+           r-affyio
+           r-biobase
+           r-biocgenerics
+           r-biostrings
+           r-dbi
+           r-ff
+           r-oligoclasses
+           r-preprocesscore
+           r-rsqlite
+           r-zlibbioc))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/oligo/")
     (synopsis "Preprocessing tools for oligonucleotide arrays")
     (description
@@ -4781,20 +5211,19 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.24.0")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "0xssanffh1hr7f48mnazcpwi25rdp7mxlyb9nbf4q2mp7m40jnpm"))))
+         "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-ggplot2" ,r-ggplot2)
-       ("r-reshape2" ,r-reshape2)))
+     (list r-ggplot2 r-reshape2))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/StoreyLab/qvalue")
     (synopsis "Q-value estimation for false discovery rate control")
     (description
@@ -4836,23 +5265,23 @@ integration with @code{Rcpp}.")
 (define-public r-apeglm
   (package
    (name "r-apeglm")
-   (version "1.14.0")
+   (version "1.16.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "apeglm" version))
             (sha256
              (base32
-              "1xld6ar440achik4dbd7vhiw6jfj0sb96jm52n7hav5bv4gag3mh"))))
+              "11w4vyc1sllmm5lh42krhidazid78n4s3lhikpy9kk2l57jmifbr"))))
    (properties `((upstream-name . "apeglm")))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-emdbook" ,r-emdbook)
-      ("r-genomicranges" ,r-genomicranges)
-      ("r-rcpp" ,r-rcpp)
-      ("r-rcppeigen" ,r-rcppeigen)
-      ("r-rcppnumerical" ,r-rcppnumerical)
-      ("r-summarizedexperiment" ,r-summarizedexperiment)))
-   (native-inputs `(("r-knitr" ,r-knitr)))
+    (list r-emdbook
+          r-genomicranges
+          r-rcpp
+          r-rcppeigen
+          r-rcppnumerical
+          r-summarizedexperiment))
+   (native-inputs (list r-knitr))
    (home-page "https://bioconductor.org/packages/apeglm")
    (synopsis "Approximate posterior estimation for GLM coefficients")
    (description "This package provides Bayesian shrinkage estimators for
@@ -4863,24 +5292,24 @@ posterior for individual coefficients.")
 (define-public r-greylistchip
   (package
    (name "r-greylistchip")
-   (version "1.24.0")
+   (version "1.26.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "GreyListChIP" version))
             (sha256
              (base32
-              "1g9ja8p90czx83ar0l9ran7m6aggvszdbqm714fq7z4rxq9b4hs3"))))
+              "1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv"))))
    (properties `((upstream-name . "GreyListChIP")))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-bsgenome" ,r-bsgenome)
-      ("r-genomeinfodb" ,r-genomeinfodb)
-      ("r-genomicalignments" ,r-genomicalignments)
-      ("r-genomicranges" ,r-genomicranges)
-      ("r-mass" ,r-mass)
-      ("r-rsamtools" ,r-rsamtools)
-      ("r-rtracklayer" ,r-rtracklayer)
-      ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (list r-bsgenome
+          r-genomeinfodb
+          r-genomicalignments
+          r-genomicranges
+          r-mass
+          r-rsamtools
+          r-rtracklayer
+          r-summarizedexperiment))
    (home-page "https://bioconductor.org/packages/GreyListChIP")
    (synopsis "Greylist artefact regions based on ChIP inputs")
    (description "This package identifies regions of ChIP experiments with high
@@ -4890,40 +5319,40 @@ signal in the input, that lead to spurious peaks during peak calling.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "3.2.7")
+    (version "3.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "01jfxcj5c0088vvsi3pz8fs0ka6n12l2j8s1d0rpqwa1y0444x7z"))))
+         "1bz03ls7pkb09p6nkz7gfnhjlh06mgbp3j98ppnzibiar3cjrnfj"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-amap" ,r-amap)
-       ("r-apeglm" ,r-apeglm)
-       ("r-ashr" ,r-ashr)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-deseq2" ,r-deseq2)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-gplots" ,r-gplots)
-       ("r-greylistchip" ,r-greylistchip)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-limma" ,r-limma)
-       ("r-locfit" ,r-locfit)
-       ("r-rcolorbrewer" , r-rcolorbrewer)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-systempiper" ,r-systempiper)))
+     (list r-amap
+           r-apeglm
+           r-ashr
+           r-biocparallel
+           r-deseq2
+           r-dplyr
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-ggrepel
+           r-gplots
+           r-greylistchip
+           r-iranges
+           r-lattice
+           r-limma
+           r-locfit
+           r-rcolorbrewer
+           r-rcpp
+           r-rhtslib
+           r-rsamtools
+           r-s4vectors
+           r-summarizedexperiment
+           r-systempiper))
     (home-page "https://bioconductor.org/packages/DiffBind")
     (synopsis "Differential binding analysis of ChIP-Seq peak data")
     (description
@@ -4946,13 +5375,13 @@ occupancy (overlap) analysis and plotting functions.")
     (properties `((upstream-name . "RIPSeeker")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-s4vectors" ,r-s4vectors)
-       ("r-iranges" ,r-iranges)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-rtracklayer" ,r-rtracklayer)))
+     (list r-s4vectors
+           r-iranges
+           r-genomicranges
+           r-summarizedexperiment
+           r-rsamtools
+           r-genomicalignments
+           r-rtracklayer))
     (home-page "https://bioconductor.org/packages/RIPSeeker")
     (synopsis
      "Identifying protein-associated transcripts from RIP-seq experiments")
@@ -4968,29 +5397,29 @@ processing to visualization and annotation.")
 (define-public r-mbkmeans
   (package
     (name "r-mbkmeans")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "mbkmeans" version))
               (sha256
                (base32
-                "1k7ngpx4s50jplrsv19zzjr7izpdl9wwppb218ih5cp0ki1gcc2n"))))
+                "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k"))))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-benchmarkme" ,r-benchmarkme)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-clusterr" ,r-clusterr)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-beachmat
+           r-benchmarkme
+           r-biocparallel
+           r-clusterr
+           r-delayedarray
+           r-matrix
+           r-rcpp
+           r-rcpparmadillo
+           r-rhdf5lib
+           r-s4vectors
+           r-singlecellexperiment
+           r-summarizedexperiment))
     (home-page "https://bioconductor.org/packages/mbkmeans")
     (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
     (description "This package implements the mini-batch k-means algorithm for
@@ -5000,20 +5429,17 @@ large datasets, including support for on-disk data representation.")
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.48.0")
+    (version "2.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "1wi15v4llgv11hpb2j9h4a35nrnawnmvbz5d5dvgy8lhqrlq8w9a"))))
+         "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-survival" ,r-survival)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biobase" ,r-biobase)
-       ("r-mass" ,r-mass)))
+     (list r-survival r-biocgenerics r-biobase r-mass))
     (home-page "https://bioconductor.org/packages/multtest")
     (synopsis "Resampling-based multiple hypothesis testing")
     (description
@@ -5038,16 +5464,16 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.70.0")
+    (version "1.72.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "1i7s198d5kw4gk6nqqsd3vqaknj4493p822f2za8q95gv6x02rxa"))))
+                "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)))
+     (list r-biocgenerics))
     (home-page "https://bioconductor.org/packages/graph")
     (synopsis "Handle graph data structures in R")
     (description
@@ -5069,8 +5495,7 @@ expressed genes in DNA microarray experiments.")
     (properties `((upstream-name . "ggm")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-graph" ,r-graph)
-       ("r-igraph" ,r-igraph)))
+     (list r-graph r-igraph))
     (home-page "https://cran.r-project.org/package=ggm")
     (synopsis "Functions for graphical Markov models")
     (description
@@ -5093,9 +5518,7 @@ fitting of some classes of graphical Markov models.")
     (properties `((upstream-name . "PerfMeas")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-graph" ,r-graph)
-       ("r-limma" ,r-limma)
-       ("r-rbgl" ,r-rbgl)))
+     (list r-graph r-limma r-rbgl))
     (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
     (synopsis "Performance measures for ranking and classification tasks")
     (description
@@ -5119,9 +5542,7 @@ a given recall, F-score for single and multiple classes are available.")
     (properties `((upstream-name . "CodeDepends")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-codetools" ,r-codetools)
-       ("r-graph" ,r-graph)
-       ("r-xml" ,r-xml)))
+     (list r-codetools r-graph r-xml))
     (home-page "https://cran.r-project.org/web/packages/CodeDepends")
     (synopsis "Analysis of R code for reproducible research and code comprehension")
     (description
@@ -5136,44 +5557,44 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.26.4")
+    (version "3.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "1iqzm7pifl9zrw3s06i6h85n1p01pd06vh1a93izyfhgybxn262d"))))
+         "05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dbi" ,r-dbi)
-       ("r-dplyr" ,r-dplyr)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-graph" ,r-graph)
-       ("r-interactionset" ,r-interactionset)
-       ("r-iranges" ,r-iranges)
-       ("r-keggrest" ,r-keggrest)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-multtest" ,r-multtest)
-       ("r-rbgl" ,r-rbgl)
-       ("r-regioner" ,r-regioner)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-venndiagram" ,r-venndiagram)))
+     (list r-annotationdbi
+           r-biocgenerics
+           r-biomart
+           r-biostrings
+           r-dbi
+           r-dplyr
+           r-ensembldb
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-graph
+           r-interactionset
+           r-iranges
+           r-keggrest
+           r-matrixstats
+           r-multtest
+           r-rbgl
+           r-regioner
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-summarizedexperiment
+           r-venndiagram))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
     (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
     (description
@@ -5190,18 +5611,18 @@ enrichedGO (addGeneIDs).")
 (define-public r-matrixgenerics
   (package
    (name "r-matrixgenerics")
-   (version "1.4.3")
+   (version "1.6.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MatrixGenerics" version))
             (sha256
              (base32
-              "1yir3rwhz5vf0pdn3fpvlc57c75k98gvv8gapajbvymz3lyghijv"))))
+              "1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3"))))
    (properties
     `((upstream-name . "MatrixGenerics")))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-matrixstats" ,r-matrixstats)))
+    (list r-matrixstats))
    (home-page "https://bioconductor.org/packages/MatrixGenerics")
    (synopsis "S4 generic summary statistic functions for matrix-like objects")
    (description
@@ -5217,15 +5638,15 @@ incompatibilities.")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.70.0")
+    (version "1.72.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "0wpmrhqpyv27h1hn31hzz21r74r7yqx79ljv8i8gn6ix8lf5ca56"))))
+               (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-limma" ,r-limma)))
+     (list r-limma))
     (home-page "https://bioconductor.org/packages/marray")
     (synopsis "Exploratory analysis for two-color spotted microarray data")
     (description "This package contains class definitions for two-color spotted
@@ -5236,17 +5657,16 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.52.0")
+   (version "1.54.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "1p87k4vw981k97d9bckmprrfg55jwd91658rgxzjj8hnschf28a4"))))
+             (base32 "1kfxw126bddfy67cmf8dca9qq4bg7fkxjf8iaikplhvs5hl7bp4d"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-biobase" ,r-biobase)
-      ("r-marray" ,r-marray)))
+    (list r-biobase r-marray))
    (home-page "https://bioconductor.org/packages/CGHbase")
    (synopsis "Base functions and classes for arrayCGH data analysis")
    (description "This package contains functions and classes that are needed by
@@ -5256,20 +5676,16 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.54.0")
+   (version "2.56.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "1zik04y2q0anzy85l0b4ryzkxpfx2fnmpwp5s7akyk1jfl2r8gw7"))))
+             (base32 "1r4y8zakgmdbnpwgp14kwh4iwqgqcmjq2yg4nc7j37p09bw1c8zr"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-biobase" ,r-biobase)
-      ("r-cghbase" ,r-cghbase)
-      ("r-impute" ,r-impute)
-      ("r-dnacopy" ,r-dnacopy)
-      ("r-snowfall" ,r-snowfall)))
+    (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
    (home-page "https://bioconductor.org/packages/CGHcall")
    (synopsis "Base functions and classes for arrayCGH data analysis")
    (description "This package contains functions and classes that are needed by
@@ -5279,26 +5695,25 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "1p4544xlarkbgs9kybrrawq3v7qr6ix62nrc6l7dcksh2ka69yzf"))))
+               (base32 "1sza9br8agpdz1k9fn5wisir44sj8v0rk4wbx35d2c2kp9q70pqj"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-cghbase" ,r-cghbase)
-       ("r-cghcall" ,r-cghcall)
-       ("r-dnacopy" ,r-dnacopy)
-       ("r-future" ,r-future)
-       ("r-future-apply" ,r-future-apply)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-r-utils" ,r-r-utils)
-       ("r-rsamtools" ,r-rsamtools)))
+     (list r-biobase
+           r-cghbase
+           r-cghcall
+           r-dnacopy
+           r-future-apply
+           r-genomicranges
+           r-iranges
+           r-matrixstats
+           r-r-utils
+           r-rsamtools))
     (home-page "https://bioconductor.org/packages/QDNAseq")
     (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
     (description "The genome is divided into non-overlapping fixed-sized bins,
@@ -5312,20 +5727,18 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "0hyc0sl2nf18bz0jxbzim0v41zwh2rnnr7l3p6zkk9wnw5gn7bbc"))))
+         "1zgxwb287ccz4wqsjxmffknnzziv12l4yrw7df912dxz6yccvd8r"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-abind" ,r-abind)
-       ("r-edger" ,r-edger)
-       ("r-genomicranges" ,r-genomicranges)))
+     (list r-abind r-edger r-genomicranges))
     (home-page "https://bioconductor.org/packages/baySeq/")
     (synopsis "Bayesian analysis of differential expression patterns in count data")
     (description
@@ -5338,27 +5751,27 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "1kfxjh1mynrgqsy2q6byf03cbymqc8w7l7672iyd0wj5qzlif4h5"))))
+         "1wdy92y5l3wa3zgg59w69rd7gdwf4z1waa4i2cccniccz463p1xq"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocgenerics
+           r-bsgenome-hsapiens-ucsc-hg19
+           r-bsgenome-mmusculus-ucsc-mm9
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-limma
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors))
     (home-page "https://bioconductor.org/packages/ChIPComp")
     (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
     (description
@@ -5372,35 +5785,35 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "1jmd8yrv7p7hn4gdibg3svmhqxjyrnfp7cgsqg8zv862lgd75zsl"))))
+         "1szlzvm8ggjc40k4z2fxxa2h28g6j9wj2g5aw480v9hgyvvdw5lx"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-data-table" ,r-data-table)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggbio" ,r-ggbio)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-plyr" ,r-plyr)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-sqldf" ,r-sqldf)))
+     (list r-biocgenerics
+           r-biostrings
+           r-data-table
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-ggbio
+           r-ggplot2
+           r-iranges
+           r-plyr
+           r-reshape2
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-sqldf))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/RiboProfiling/")
     (synopsis "Ribosome profiling data analysis")
     (description "Starting with a BAM file, this package provides the
@@ -5413,24 +5826,24 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "1m5w2j35wr0lzwir4s58z757vrcsj5mglsqrkvs241k0hlmn06qa"))))
+         "0nnhjvjl4c9yyfzjf8kcj4yky5cdimicp7lz008sczy19jq4vjhd"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-abind" ,r-abind)
-       ("r-bayseq" ,r-bayseq)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-seqlogo" ,r-seqlogo)))
+     (list r-abind
+           r-bayseq
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-rsamtools
+           r-seqlogo))
     (home-page "https://bioconductor.org/packages/riboSeqR/")
     (synopsis "Analysis of sequencing data from ribosome profiling experiments")
     (description
@@ -5441,28 +5854,28 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb"))))
+         "19m2mpby73zanai68rlqvzx9zccli4dz4kix93acrw9755xp3bsw"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-biocgenerics
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-matrix
+           r-rcpp
+           r-s4vectors
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/InteractionSet")
     (synopsis "Base classes for storing genomic interaction data")
     (description
@@ -5475,36 +5888,36 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0zjl7rp5fk14kqsx0bkbpq6hqahbkiyvwa9aggp4kfb8hnmz9qal"))))
+         "090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-data-table" ,r-data-table)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-gviz" ,r-gviz)
-       ("r-igraph" ,r-igraph)
-       ("r-interactionset" ,r-interactionset)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-stringr" ,r-stringr)))
+     (list r-biobase
+           r-biocgenerics
+           r-data-table
+           r-dplyr
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-gridextra
+           r-gviz
+           r-igraph
+           r-interactionset
+           r-iranges
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-stringr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
     (synopsis "R package for handling genomic interaction data")
     (description
@@ -5516,16 +5929,16 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "1v8aysvy6a3r1iafc3xvk885c128kb3pb9zpcdhdjcn0by96k8hh"))))
+         "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx"))))
     (build-system r-build-system)
-    (propagated-inputs `(("r-amap" ,r-amap)))
+    (propagated-inputs (list r-amap))
     (home-page "https://bioconductor.org/packages/ctc/")
     (synopsis "Cluster and tree conversion")
     (description
@@ -5536,22 +5949,22 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "07qrxssx4rb8r958r1smx8xfpzdxpp55hci3201hcmz3mxz77i0s"))))
+         "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biasedurn" ,r-biasedurn)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genelendatabase" ,r-genelendatabase)
-       ("r-go-db" ,r-go-db)
-       ("r-mgcv" ,r-mgcv)))
+     (list r-annotationdbi
+           r-biasedurn
+           r-biocgenerics
+           r-genelendatabase
+           r-go-db
+           r-mgcv))
     (home-page "https://bioconductor.org/packages/goseq/")
     (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
     (description
@@ -5562,26 +5975,26 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "0dsk8qmwimzmd1x4k4jwg9q11jm1ahn8cw0gzd6s2gmigfls4hsa"))))
+         "0qkbx9n2vb7kvb5f00csnbffy5bm7hhbdvkx2isgzi0wv0y59kx9"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-deseq2" ,r-deseq2)
-       ("r-edger" ,r-edger)
-       ("r-htmlwidgets" ,r-htmlwidgets)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-limma" ,r-limma)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-deseq2
+           r-edger
+           r-htmlwidgets
+           r-jsonlite
+           r-limma
+           r-s4vectors
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/Shians/Glimma")
     (synopsis "Interactive HTML graphics")
     (description
@@ -5595,19 +6008,18 @@ information.")
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "18wyi73l95df182vg3m014sxwdbpggr61vsbazhyw4vyx2fnzmpl"))))
+         "0qhy984y83a3nf4zw54rasw3vn932q4zb3gljifkw701jnrzqmki"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-rcpp" ,r-rcpp)))
+     (list r-biobase r-rcpp))
     (home-page "https://bioconductor.org/packages/ROTS/")
     (synopsis "Reproducibility-Optimized Test Statistic")
     (description
@@ -5619,18 +6031,17 @@ in omics data.")
 (define-public r-plgem
   (package
     (name "r-plgem")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "plgem" version))
        (sha256
         (base32
-         "1rz5jk5bgpk7gjknx79jyslahjg46q2f4bx6dgd0vwmarc29a45z"))))
+         "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-mass" ,r-mass)))
+     (list r-biobase r-mass))
     (home-page "http://www.genopolis.it")
     (synopsis "Detect differential expression in microarray and proteomics datasets")
     (description
@@ -5644,41 +6055,40 @@ genes or proteins in these datasets.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "0jh5db9dv5pb6b50sg22x8q55m3h0h0nkmb9mivvvp22dhyrd82z"))))
+         "072kv5k3giyll1clzrg0anqhyl4qbi7cjnmkqz25zdl5bab9l7jk"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-deseq2" ,r-deseq2)
-       ("r-desolve" ,r-desolve)
-       ("r-gdata" ,r-gdata)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-plgem" ,r-plgem)
-       ("r-proc" ,r-proc)
-       ("r-rootsolve" ,r-rootsolve)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-txdb-mmusculus-ucsc-mm9-knowngene"
-        ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
+     (list r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-deseq2
+           r-desolve
+           r-gdata
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-kernsmooth
+           r-plgem
+           r-proc
+           r-rootsolve
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-shiny
+           r-summarizedexperiment
+           r-txdb-mmusculus-ucsc-mm9-knowngene))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/INSPEcT")
     (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
     (description
@@ -5691,22 +6101,20 @@ modeling the rates that determines changes in mature mRNA levels.")
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp"))))
+         "07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bh" ,r-bh)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)))
+     (list r-bh r-matrix r-rcpp))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/DNABarcodes")
     (synopsis "Create and analyze DNA barcodes")
     (description
@@ -5720,23 +6128,20 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 (define-public r-ruvseq
   (package
     (name "r-ruvseq")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RUVSeq" version))
        (sha256
         (base32
-         "1fy0k1p0m209lzjpd5jhfnifa22lrn63qq3a3kn5g0xhbbmijzac"))))
+         "1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q"))))
     (properties `((upstream-name . "RUVSeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-edaseq" ,r-edaseq)
-       ("r-edger" ,r-edger)
-       ("r-mass" ,r-mass)))
+     (list r-biobase r-edaseq r-edger r-mass))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/drisso/RUVSeq")
     (synopsis "Remove unwanted variation from RNA-Seq data")
     (description
@@ -5748,24 +6153,20 @@ samples.")
 (define-public r-biocneighbors
   (package
     (name "r-biocneighbors")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocNeighbors" version))
        (sha256
         (base32
-         "0cjidi18wjip9xzx83890wjk40vvjq06prf1ag4m2kac47w01r7v"))))
+         "04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr"))))
     (properties `((upstream-name . "BiocNeighbors")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpphnsw" ,r-rcpphnsw)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiocNeighbors")
     (synopsis "Nearest Neighbor Detection for Bioconductor packages")
     (description
@@ -5780,21 +6181,19 @@ achieved for all methods using the BiocParallel framework.")
 (define-public r-scaledmatrix
   (package
     (name "r-scaledmatrix")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ScaledMatrix" version))
        (sha256
         (base32
-         "1j96fvw1waqxbv5c8myfmhsidq370z03yz13yqmrs4nn1rpn1a06"))))
+         "0vz8441gl5gycy1ypybwhq97bnyvhhlg6gxpi1dsdy2c9b6d81kc"))))
     (properties `((upstream-name . "ScaledMatrix")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-delayedarray" ,r-delayedarray)
-       ("r-matrix" ,r-matrix)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-delayedarray r-matrix r-s4vectors))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/LTLA/ScaledMatrix")
     (synopsis "Create a DelayedMatrix of scaled and centered values")
     (description
@@ -5808,25 +6207,25 @@ multiplication.")
 (define-public r-treeio
   (package
     (name "r-treeio")
-    (version "1.16.2")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "treeio" version))
        (sha256
         (base32
-         "1y60yvg1rl21cab9xrkns0209pg44mwr90qj099dvk97wsjkx67g"))))
+         "19i8jhvycv57zbxhpn5gx5ymdiws64kc3nidc00xh1j9a8xkj1aq"))))
     (properties `((upstream-name . "treeio")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-ape" ,r-ape)
-       ("r-dplyr" ,r-dplyr)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-magrittr" ,r-magrittr)
-       ("r-rlang" ,r-rlang)
-       ("r-tibble" ,r-tibble)
-       ("r-tidytree" ,r-tidytree)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-ape
+           r-dplyr
+           r-jsonlite
+           r-magrittr
+           r-rlang
+           r-tibble
+           r-tidytree))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/YuLab-SMU/treeio")
     (synopsis "Base classes and functions for Phylogenetic tree input and output")
     (description
@@ -5840,31 +6239,31 @@ platform for merging tree with associated data and converting file formats.")
 (define-public r-ggtree
   (package
     (name "r-ggtree")
-    (version "3.0.4")
+    (version "3.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggtree" version))
        (sha256
         (base32
-         "0xf4b9vfdyzzivwgw4ymapl5bb4k9p04mmr53822kxgfd5qrs1zx"))))
+         "0qk39gdpy4kznjhmvi25y2spcdj2r1i6mv673vx8dzf66zfs20v8"))))
     (properties `((upstream-name . "ggtree")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-ape" ,r-ape)
-       ("r-aplot" ,r-aplot)
-       ("r-dplyr" ,r-dplyr)
-       ("r-ggfun" ,r-ggfun)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-magrittr" ,r-magrittr)
-       ("r-purrr" ,r-purrr)
-       ("r-rlang" ,r-rlang)
-       ("r-scales" ,r-scales)
-       ("r-tidyr" ,r-tidyr)
-       ("r-tidytree" ,r-tidytree)
-       ("r-treeio" ,r-treeio)
-       ("r-yulab-utils" ,r-yulab-utils)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-ape
+           r-aplot
+           r-dplyr
+           r-ggfun
+           r-ggplot2
+           r-magrittr
+           r-purrr
+           r-rlang
+           r-scales
+           r-tidyr
+           r-tidytree
+           r-treeio
+           r-yulab-utils))
+    (native-inputs (list r-knitr))
     (home-page "https://yulab-smu.top/treedata-book/")
     (synopsis "R package for visualization of trees and annotation data")
     (description
@@ -5877,20 +6276,20 @@ data.")
 (define-public r-metapod
   (package
     (name "r-metapod")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "metapod" version))
        (sha256
         (base32
-         "1hbcwr6d8gyrf4azh0gi588xkrg6gz7gsb5hbvzqkhplbsp6shlv"))))
+         "1s8dfzpgbpxbn3jvx891gvw3jyn43nlxb73yv1vjn85brk9zbqpk"))))
     (properties `((upstream-name . "metapod")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-rcpp" ,r-rcpp)))
+     (list r-rcpp))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/metapod")
     (synopsis "Meta-analyses on p-values of differential analyses")
     (description
@@ -5906,29 +6305,29 @@ missing values and weighting where appropriate.")
 (define-public r-biocsingular
   (package
     (name "r-biocsingular")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSingular" version))
        (sha256
         (base32
-         "16gkwq8fb8jdchpnlzq2hz3i74a6pzbnc1bf93282h11mp7qr58l"))))
+         "0dkh6a23qymjcynppmpp3k1mzpfadv8dqyz410pxkqsxig4ldd4n"))))
     (properties `((upstream-name . "BiocSingular")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-irlba" ,r-irlba)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rsvd" ,r-rsvd)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scaledmatrix" ,r-scaledmatrix)))
+     (list r-beachmat
+           r-biocgenerics
+           r-biocparallel
+           r-delayedarray
+           r-irlba
+           r-matrix
+           r-rcpp
+           r-rsvd
+           r-s4vectors
+           r-scaledmatrix))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/LTLA/BiocSingular")
     (synopsis "Singular value decomposition for Bioconductor packages")
     (description
@@ -5941,40 +6340,40 @@ possible, parallelization is achieved using the BiocParallel framework.")
 (define-public r-destiny
   (package
     (name "r-destiny")
-    (version "3.4.0")
+    (version "3.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "destiny" version))
        (sha256
         (base32
-         "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
+         "01662p5j9l12ylf5a5djg4cjppd2n3chrygzw8nnrcf1806xn58y"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-ggplot-multistats" ,r-ggplot-multistats)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggthemes" ,r-ggthemes)
-       ("r-irlba" ,r-irlba)
-       ("r-knn-covertree" ,r-knn-covertree)
-       ("r-matrix" ,r-matrix)
-       ("r-pcamethods" ,r-pcamethods)
-       ("r-proxy" ,r-proxy)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcppeigen" ,r-rcppeigen)
-       ("r-rcpphnsw" ,r-rcpphnsw)
-       ("r-rspectra" ,r-rspectra)
-       ("r-scales" ,r-scales)
-       ("r-scatterplot3d" ,r-scatterplot3d)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-smoother" ,r-smoother)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-tidyr" ,r-tidyr)
-       ("r-tidyselect" ,r-tidyselect)
-       ("r-vim" ,r-vim)))
+     (list r-biobase
+           r-biocgenerics
+           r-ggplot-multistats
+           r-ggplot2
+           r-ggthemes
+           r-irlba
+           r-knn-covertree
+           r-matrix
+           r-pcamethods
+           r-proxy
+           r-rcpp
+           r-rcppeigen
+           r-rcpphnsw
+           r-rspectra
+           r-scales
+           r-scatterplot3d
+           r-singlecellexperiment
+           r-smoother
+           r-summarizedexperiment
+           r-tidyr
+           r-tidyselect
+           r-vim))
     (native-inputs
-     `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
+     (list r-nbconvertr)) ; for vignettes
     (home-page "https://bioconductor.org/packages/destiny/")
     (synopsis "Create and plot diffusion maps")
     (description "This package provides tools to create and plot diffusion
@@ -5985,22 +6384,18 @@ maps.")
 (define-public r-savr
   (package
     (name "r-savr")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "savR" version))
        (sha256
         (base32
-         "1ynp334hm76zf05j4f6vha6r16s5f2ncxx9yviq4rxidk9r723jq"))))
+         "0dwl94j5dm5ngn8lyyc4bd9ihd1nqincvq26najjn6lw0x55ciky"))))
     (properties `((upstream-name . "savR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-reshape2" ,r-reshape2)
-       ("r-scales" ,r-scales)
-       ("r-xml" ,r-xml)))
+     (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
     (home-page "https://github.com/bcalder/savR")
     (synopsis "Parse and analyze Illumina SAV files")
     (description
@@ -6011,36 +6406,36 @@ Viewer (SAV) files, access data, and generate QC plots.")
 (define-public r-chipexoqual
   (package
     (name "r-chipexoqual")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPexoQual" version))
        (sha256
         (base32
-         "0fbrf5s6pz115djm7xw95k1d0p7svi40aacbb3d52wmx5azwj424"))))
+         "1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk"))))
     (properties `((upstream-name . "ChIPexoQual")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-broom" ,r-broom)
-       ("r-data-table" ,r-data-table)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-hexbin" ,r-hexbin)
-       ("r-iranges" ,r-iranges)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-viridis" ,r-viridis)))
+     (list r-biocparallel
+           r-biovizbase
+           r-broom
+           r-data-table
+           r-dplyr
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-hexbin
+           r-iranges
+           r-rcolorbrewer
+           r-rmarkdown
+           r-rsamtools
+           r-s4vectors
+           r-scales
+           r-viridis))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/keleslab/ChIPexoQual")
     (synopsis "Quality control pipeline for ChIP-exo/nexus data")
     (description
@@ -6051,19 +6446,16 @@ sequencing data.")
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "03pvjzjrcsbjfw3855s3whfzin45vaipy7cahnj6fywdysvh8hps"))))
+                "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-s4vectors" ,r-s4vectors)
-       ("r-iranges" ,r-iranges)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-biocgenerics" ,r-biocgenerics)))
+     (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
     (home-page "https://bioconductor.org/packages/copynumber")
     (synopsis "Segmentation of single- and multi-track copy number data")
     (description
@@ -6074,17 +6466,17 @@ penalized least squares regression method.")
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNAcopy" version))
        (sha256
         (base32
-         "0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d"))))
+         "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm"))))
     (properties `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
-    (native-inputs `(("gfortran" ,gfortran)))
+    (native-inputs (list gfortran))
     (home-page "https://bioconductor.org/packages/DNAcopy")
     (synopsis "DNA copy number data analysis")
     (description
@@ -6109,9 +6501,7 @@ abnormal copy number.")
     (properties `((upstream-name . "HTSCluster")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-capushe" ,r-capushe)
-       ("r-edger" ,r-edger)
-       ("r-plotrix" ,r-plotrix)))
+     (list r-capushe r-edger r-plotrix))
     (home-page "https://cran.r-project.org/web/packages/HTSCluster")
     (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
     (description
@@ -6163,7 +6553,7 @@ and summarizing a set of statistics using a weighted distance approach.")
     (properties `((upstream-name . "NBPSeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-qvalue" ,r-qvalue)))
+     (list r-qvalue))
     (home-page "https://cran.r-project.org/web/packages/NBPSeq")
     (synopsis "Negative binomial models for RNA-Seq data")
     (description
@@ -6174,20 +6564,18 @@ and regression inferences from RNA-sequencing data.")
 (define-public r-ebseq
   (package
     (name "r-ebseq")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBSeq" version))
        (sha256
         (base32
-         "0h5v3vrb90zim80bdnr3aw58g3h7zjqa4l9i0jwx5j19ywf54fdz"))))
+         "1p8i04v5h6mbc8zqbf3rifbwwylzzc1fqrkhh0a0mbcgq2nv7i9m"))))
     (properties `((upstream-name . "EBSeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-blockmodeling" ,r-blockmodeling)
-       ("r-gplots" ,r-gplots)
-       ("r-testthat" ,r-testthat)))
+     (list r-blockmodeling r-gplots r-testthat))
     (home-page "https://bioconductor.org/packages/EBSeq")
     (synopsis "Differential expression analysis of RNA-seq data")
     (description
@@ -6198,32 +6586,32 @@ gene and isoform level using RNA-seq data")
 (define-public r-karyoploter
   (package
     (name "r-karyoploter")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "karyoploteR" version))
               (sha256
                (base32
-                "11sgxz2xz685pgm8mf0hzm6aryx4fj5g3dlffjzpqxh3awfqa19p"))))
+                "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-bamsignals" ,r-bamsignals)
-       ("r-bezier" ,r-bezier)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-digest" ,r-digest)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-memoise" ,r-memoise)
-       ("r-regioner" ,r-regioner)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-annotationdbi
+           r-bamsignals
+           r-bezier
+           r-biovizbase
+           r-digest
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-memoise
+           r-regioner
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-variantannotation))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/karyoploteR/")
     (synopsis "Plot customizable linear genomes displaying arbitrary data")
     (description "This package creates karyotype plots of arbitrary genomes and
@@ -6236,20 +6624,19 @@ coordinates.")
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lpsymphony" version))
        (sha256
         (base32
-         "0aw4b3p5z8ys7zlwy8s3bsqk03xwx42311yxr7q14w3f7sn3shzn"))))
+         "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs"))))
     (build-system r-build-system)
     (inputs
-     `(("zlib" ,zlib)))
+     (list zlib))
     (native-inputs
-     `(("pkg-config" ,pkg-config)
-       ("r-knitr" ,r-knitr)))
+     (list pkg-config r-knitr))
     (home-page "https://r-forge.r-project.org/projects/rsymphony")
     (synopsis "Symphony integer linear programming solver in R")
     (description
@@ -6266,23 +6653,20 @@ to install interface to SYMPHONY.")
 (define-public r-ihw
   (package
     (name "r-ihw")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IHW" version))
        (sha256
         (base32
-         "0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw"))))
+         "0vgij5zyaw3fh7arkg4jy1mizsqzbkcsjl05mh3ng2bqh30kyqqx"))))
     (properties `((upstream-name . "IHW")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-fdrtool" ,r-fdrtool)
-       ("r-lpsymphony" ,r-lpsymphony)
-       ("r-slam" ,r-slam)))
+     (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/IHW")
     (synopsis "Independent hypothesis weighting")
     (description
@@ -6298,30 +6682,30 @@ independent of the p-value under the null hypothesis.")
 (define-public r-icobra
   (package
     (name "r-icobra")
-    (version "1.20.0")
+    (version "1.22.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iCOBRA" version))
        (sha256
         (base32
-         "190rkx3sivj68in36hhin5v535yd6fvlvm7l90w1bl38zpb7p6jn"))))
+         "1ln8l2cp6dqg6zv7s0qnmw5ii93v5sgp0b1nwswl52zdd8mivwxy"))))
     (properties `((upstream-name . "iCOBRA")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-dplyr" ,r-dplyr)
-       ("r-dt" ,r-dt)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-limma" ,r-limma)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rocr" ,r-rocr)
-       ("r-scales" ,r-scales)
-       ("r-shiny" ,r-shiny)
-       ("r-shinybs" ,r-shinybs)
-       ("r-shinydashboard" ,r-shinydashboard)
-       ("r-upsetr" ,r-upsetr)))
+     (list r-dplyr
+           r-dt
+           r-ggplot2
+           r-limma
+           r-reshape2
+           r-rocr
+           r-scales
+           r-shiny
+           r-shinybs
+           r-shinydashboard
+           r-upsetr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/iCOBRA")
     (synopsis "Comparison and visualization of ranking and assignment methods")
     (description
@@ -6334,23 +6718,21 @@ interactive exploration of results.")
 (define-public r-residualmatrix
   (package
     (name "r-residualmatrix")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ResidualMatrix" version))
        (sha256
         (base32
-         "0p7va19aw0j6anx7ck879kbi5cn7dy712h5ia94adr38ssismv1v"))))
+         "0xsn4fm34a7xpkgmx3a1j2xzdaxf2hyla1062wqn04kw0k9y29vg"))))
     (properties
      `((upstream-name . "ResidualMatrix")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-delayedarray" ,r-delayedarray)
-       ("r-matrix" ,r-matrix)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-delayedarray r-matrix r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/LTLA/ResidualMatrix")
     (synopsis "Create a DelayedMatrix of regression residuals")
     (description
@@ -6365,34 +6747,34 @@ multiplication and calculation of row/column sums or means.")
 (define-public r-batchelor
   (package
     (name "r-batchelor")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "batchelor" version))
        (sha256
         (base32
-         "1bkk69b5llkmvmpsnhymwjm2szmzypgszfsw8mak1b5ms5zf8lr0"))))
+         "0axkic11bwjbw8apwxx6p51s7jvlwhq7xi1bdknn54k86axq84dr"))))
     (properties `((upstream-name . "batchelor")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocneighbors" ,r-biocneighbors)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biocsingular" ,r-biocsingular)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-igraph" ,r-igraph)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-residualmatrix" ,r-residualmatrix)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scaledmatrix" ,r-scaledmatrix)
-       ("r-scuttle" ,r-scuttle)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-beachmat
+           r-biocgenerics
+           r-biocneighbors
+           r-biocparallel
+           r-biocsingular
+           r-delayedarray
+           r-delayedmatrixstats
+           r-igraph
+           r-matrix
+           r-rcpp
+           r-residualmatrix
+           r-s4vectors
+           r-scaledmatrix
+           r-scuttle
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/batchelor")
     (synopsis "Single-Cell Batch Correction Methods")
     (description
@@ -6408,31 +6790,31 @@ the numbers of cells across batches.")
 (define-public r-mast
   (package
     (name "r-mast")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MAST" version))
        (sha256
         (base32
-         "1gkpagam5rap36viyr3n4psa658x9vckrxap1h67jasiiyrcfz2d"))))
+         "14h6giny9lhzqjsx3h7gdhsm8wfwnvp5zsl4avrflip0jmsn45yy"))))
     (properties `((upstream-name . "MAST")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-abind" ,r-abind)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-data-table" ,r-data-table)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-plyr" ,r-plyr)
-       ("r-progress" ,r-progress)
-       ("r-reshape2" ,r-reshape2)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-stringr" ,r-stringr)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-abind
+           r-biobase
+           r-biocgenerics
+           r-data-table
+           r-ggplot2
+           r-plyr
+           r-progress
+           r-reshape2
+           r-s4vectors
+           r-singlecellexperiment
+           r-stringr
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/RGLab/MAST/")
     (synopsis "Model-based analysis of single cell transcriptomics")
     (description
@@ -6443,48 +6825,48 @@ single cell assay data.")
 (define-public r-monocle
   (package
     (name "r-monocle")
-    (version "2.20.0")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "monocle" version))
        (sha256
         (base32
-         "05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry"))))
+         "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocviews" ,r-biocviews)
-       ("r-cluster" ,r-cluster)
-       ("r-combinat" ,r-combinat)
-       ("r-ddrtree" ,r-ddrtree)
-       ("r-densityclust" ,r-densityclust)
-       ("r-dplyr" ,r-dplyr)
-       ("r-fastica" ,r-fastica)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-hsmmsinglecell" ,r-hsmmsinglecell)
-       ("r-igraph" ,r-igraph)
-       ("r-irlba" ,r-irlba)
-       ("r-limma" ,r-limma)
-       ("r-mass" ,r-mass)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-pheatmap" ,r-pheatmap)
-       ("r-plyr" ,r-plyr)
-       ("r-proxy" ,r-proxy)
-       ("r-qlcmatrix" ,r-qlcmatrix)
-       ("r-rann" ,r-rann)
-       ("r-rcpp" ,r-rcpp)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rtsne" ,r-rtsne)
-       ("r-slam" ,r-slam)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-vgam" ,r-vgam)
-       ("r-viridis" ,r-viridis)))
+     (list r-biobase
+           r-biocgenerics
+           r-biocviews
+           r-cluster
+           r-combinat
+           r-ddrtree
+           r-densityclust
+           r-dplyr
+           r-fastica
+           r-ggplot2
+           r-hsmmsinglecell
+           r-igraph
+           r-irlba
+           r-limma
+           r-mass
+           r-matrix
+           r-matrixstats
+           r-pheatmap
+           r-plyr
+           r-proxy
+           r-qlcmatrix
+           r-rann
+           r-rcpp
+           r-reshape2
+           r-rtsne
+           r-slam
+           r-stringr
+           r-tibble
+           r-vgam
+           r-viridis))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/monocle")
     (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
     (description
@@ -6516,11 +6898,11 @@ qPCR data, but could be used with other types as well.")
       (properties `((upstream-name . "leidenbase")))
       (build-system r-build-system)
       (inputs
-       `(("zlib" ,zlib)))
+       (list zlib))
       (native-inputs
-       `(("gfortran" ,gfortran)))
+       (list gfortran))
       (propagated-inputs
-       `(("r-igraph" ,r-igraph)))
+       (list r-igraph))
       (home-page "https://github.com/cole-trapnell-lab/leidenbase")
       (synopsis "R and C wrappers to run the Leiden find_partition function")
       (description
@@ -6531,6 +6913,34 @@ required source code files from the official Leidenalg distribution and
 several functions from the R igraph package.")
       (license license:gpl3+))))
 
+(define-public r-sanssouci
+  ;; sansscouci doesn't have a (versioned) release yet.
+  ;; This is the latest commit as of packaging for Guix.
+  (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f")
+        (revision "1"))
+    (package
+      (name "r-sanssouci")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/pneuvial/sanssouci.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk"))))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
+      (home-page "https://pneuvial.github.io/sanssouci")
+      (synopsis "Post Hoc multiple testing inference")
+      (description
+       "The goal of sansSouci is to perform post hoc inference: in a multiple
+testing context, sansSouci provides statistical guarantees on possibly
+user-defined and/or data-driven sets of hypotheses.")
+      (license license:gpl3))))
+
 (define-public r-monocle3
   (package
     (name "r-monocle3")
@@ -6547,50 +6957,50 @@ several functions from the R igraph package.")
          "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-assertthat" ,r-assertthat)
-       ("r-batchelor" ,r-batchelor)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-dplyr" ,r-dplyr)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-grr" ,r-grr)
-       ("r-htmlwidgets" ,r-htmlwidgets)
-       ("r-igraph" ,r-igraph)
-       ("r-irlba" ,r-irlba)
-       ("r-leidenbase" ,r-leidenbase)
-       ("r-limma" ,r-limma)
-       ("r-lmtest" ,r-lmtest)
-       ("r-mass" ,r-mass)
-       ("r-matrix" ,r-matrix)
-       ("r-matrix-utils" ,r-matrix-utils)
-       ("r-pbapply" ,r-pbapply)
-       ("r-pbmcapply" ,r-pbmcapply)
-       ("r-pheatmap" ,r-pheatmap)
-       ("r-plotly" ,r-plotly)
-       ("r-pryr" ,r-pryr)
-       ("r-proxy" ,r-proxy)
-       ("r-pscl" ,r-pscl)
-       ("r-purrr" ,r-purrr)
-       ("r-rann" ,r-rann)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcppparallel" ,r-rcppparallel)
-       ("r-reshape2" ,r-reshape2)
-       ("r-reticulate" ,r-reticulate)
-       ("r-rhpcblasctl" ,r-rhpcblasctl)
-       ("r-rsample" ,r-rsample)
-       ("r-rtsne" ,r-rtsne)
-       ("r-shiny" ,r-shiny)
-       ("r-slam" ,r-slam)
-       ("r-spdep" ,r-spdep)
-       ("r-speedglm" ,r-speedglm)
-       ("r-stringr" ,r-stringr)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)
-       ("r-uwot" ,r-uwot)
-       ("r-viridis" ,r-viridis)))
+     (list r-assertthat
+           r-batchelor
+           r-biobase
+           r-biocgenerics
+           r-delayedmatrixstats
+           r-dplyr
+           r-ggplot2
+           r-ggrepel
+           r-grr
+           r-htmlwidgets
+           r-igraph
+           r-irlba
+           r-leidenbase
+           r-limma
+           r-lmtest
+           r-mass
+           r-matrix
+           r-matrix-utils
+           r-pbapply
+           r-pbmcapply
+           r-pheatmap
+           r-plotly
+           r-pryr
+           r-proxy
+           r-pscl
+           r-purrr
+           r-rann
+           r-rcpp
+           r-rcppparallel
+           r-reshape2
+           r-reticulate
+           r-rhpcblasctl
+           r-rsample
+           r-rtsne
+           r-shiny
+           r-slam
+           r-spdep
+           r-speedglm
+           r-stringr
+           r-singlecellexperiment
+           r-tibble
+           r-tidyr
+           r-uwot
+           r-viridis))
     (home-page "https://github.com/cole-trapnell-lab/monocle3")
     (synopsis "Analysis toolkit for single-cell RNA-Seq data")
     (description
@@ -6600,19 +7010,18 @@ several functions from the R igraph package.")
 (define-public r-noiseq
   (package
     (name "r-noiseq")
-    (version "2.36.0")
+    (version "2.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "NOISeq" version))
        (sha256
         (base32
-         "18d51dv2ygsm7kkwal341f1wrwrazyns0045j00vld367kic8jiz"))))
+         "0mmvzf8y4gm84hgjdpf86b1y37237wp5mc3x1g6sdiz9qi8l356v"))))
     (properties `((upstream-name . "NOISeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-matrix" ,r-matrix)))
+     (list r-biobase r-matrix))
     (home-page "https://bioconductor.org/packages/NOISeq")
     (synopsis "Exploratory analysis and differential expression for RNA-seq data")
     (description
@@ -6627,30 +7036,30 @@ assumptions.")
 (define-public r-scdd
   (package
     (name "r-scdd")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDD" version))
        (sha256
         (base32
-         "1dw9m3m99apmbs32461c6lnmy81n5hxbhz3p8jk419gajkh4v1ji"))))
+         "0gjdjkpkm9zc9hzzb6r2mknl4zyg7s2lgqppmzzhgcnvlmgvm5b5"))))
     (properties `((upstream-name . "scDD")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-arm" ,r-arm)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-ebseq" ,r-ebseq)
-       ("r-fields" ,r-fields)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-mclust" ,r-mclust)
-       ("r-outliers" ,r-outliers)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scran" ,r-scran)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-arm
+           r-biocparallel
+           r-ebseq
+           r-fields
+           r-ggplot2
+           r-mclust
+           r-outliers
+           r-s4vectors
+           r-scran
+           r-singlecellexperiment
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/kdkorthauer/scDD")
     (synopsis "Mixture modeling of single-cell RNA-seq data")
     (description
@@ -6665,39 +7074,39 @@ distributions.")
 (define-public r-scone
   (package
     (name "r-scone")
-    (version "1.16.1")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scone" version))
        (sha256
         (base32
-         "0zw8g4mql7b02xqwhc1i0bnhm20c1q9xqc7yz84j98pqbi996vi5"))))
+         "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-aroma-light" ,r-aroma-light)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-boot" ,r-boot)
-       ("r-class" ,r-class)
-       ("r-cluster" ,r-cluster)
-       ("r-compositions" ,r-compositions)
-       ("r-diptest" ,r-diptest)
-       ("r-edger" ,r-edger)
-       ("r-fpc" ,r-fpc)
-       ("r-gplots" ,r-gplots)
-       ("r-hexbin" ,r-hexbin)
-       ("r-limma" ,r-limma)
-       ("r-matrixgenerics" ,r-matrixgenerics)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-mixtools" ,r-mixtools)
-       ("r-rarpack" ,r-rarpack)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rhdf5" ,r-rhdf5)
-       ("r-ruvseq" ,r-ruvseq)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-aroma-light
+           r-biocparallel
+           r-boot
+           r-class
+           r-cluster
+           r-compositions
+           r-diptest
+           r-edger
+           r-fpc
+           r-gplots
+           r-hexbin
+           r-limma
+           r-matrixgenerics
+           r-matrixstats
+           r-mixtools
+           r-rarpack
+           r-rcolorbrewer
+           r-rhdf5
+           r-ruvseq
+           r-singlecellexperiment
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/scone")
     (synopsis "Single cell overview of normalized expression data")
     (description
@@ -6709,27 +7118,29 @@ high-throughput analyses.")
 (define-public r-geoquery
   (package
     (name "r-geoquery")
-    (version "2.60.0")
+    (version "2.62.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GEOquery" version))
        (sha256
         (base32
-         "0jhkdbcd03d5n8vn3xkad6f21xjkawyxc9rdwcj8vwc8alx730am"))))
+         "0plmh4x37r848g6ilvl1x8cim90rp85gikfc5m8lgi2i4xkq7hbq"))))
     (properties `((upstream-name . "GEOquery")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-dplyr" ,r-dplyr)
-       ("r-httr" ,r-httr)
-       ("r-limma" ,r-limma)
-       ("r-magrittr" ,r-magrittr)
-       ("r-readr" ,r-readr)
-       ("r-tidyr" ,r-tidyr)
-       ("r-xml2" ,r-xml2)))
+     (list r-biobase
+           r-data-table
+           r-dplyr
+           r-httr
+           r-limma
+           r-magrittr
+           r-r-utils
+           r-readr
+           r-tidyr
+           r-xml2))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/seandavi/GEOquery/")
     (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
     (description
@@ -6742,17 +7153,17 @@ the bridge between GEO and BioConductor.")
 (define-public r-illuminaio
   (package
     (name "r-illuminaio")
-    (version "0.34.0")
+    (version "0.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "illuminaio" version))
        (sha256
         (base32
-         "1sy0i3nbzsw4ymdxaiwpyx1vcg9yp3i8xfjcymqwhv95j3kyglv9"))))
+         "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-base64" ,r-base64)))
+     (list r-base64))
     (home-page "https://github.com/HenrikBengtsson/illuminaio/")
     (synopsis "Parse Illumina microarray output files")
     (description
@@ -6763,19 +7174,17 @@ files, including IDAT.")
 (define-public r-siggenes
   (package
     (name "r-siggenes")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "siggenes" version))
        (sha256
         (base32
-         "0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf"))))
+         "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-multtest" ,r-multtest)
-       ("r-scrime" ,r-scrime)))
+     (list r-biobase r-multtest r-scrime))
     (home-page "https://bioconductor.org/packages/siggenes/")
     (synopsis
      "Multiple testing using SAM and Efron's empirical Bayes approaches")
@@ -6789,29 +7198,29 @@ Bayes Analyses of Microarrays} (EBAM).")
 (define-public r-bumphunter
   (package
     (name "r-bumphunter")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bumphunter" version))
        (sha256
         (base32
-         "0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v"))))
+         "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-dorng" ,r-dorng)
-       ("r-foreach" ,r-foreach)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-iterators" ,r-iterators)
-       ("r-limma" ,r-limma)
-       ("r-locfit" ,r-locfit)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-annotationdbi
+           r-biocgenerics
+           r-dorng
+           r-foreach
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-iterators
+           r-limma
+           r-locfit
+           r-matrixstats
+           r-s4vectors))
     (home-page "https://github.com/ririzarr/bumphunter")
     (synopsis "Find bumps in genomic data")
     (description
@@ -6823,47 +7232,47 @@ studies.")
 (define-public r-minfi
   (package
     (name "r-minfi")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minfi" version))
        (sha256
         (base32
-         "189lzppvrz6bw2kpppawgsfjyh2ahyy8bi9z8srpas67qf2r8jmj"))))
+         "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-beanplot" ,r-beanplot)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bumphunter" ,r-bumphunter)
-       ("r-data-table" ,r-data-table)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-genefilter" ,r-genefilter)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-geoquery" ,r-geoquery)
-       ("r-hdf5array" ,r-hdf5array)
-       ("r-illuminaio" ,r-illuminaio)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-limma" ,r-limma)
-       ("r-mass" ,r-mass)
-       ("r-mclust" ,r-mclust)
-       ("r-nlme" ,r-nlme)
-       ("r-nor1mix" ,r-nor1mix)
-       ("r-preprocesscore" ,r-preprocesscore)
-       ("r-quadprog" ,r-quadprog)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-reshape" ,r-reshape)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-siggenes" ,r-siggenes)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-beanplot
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-bumphunter
+           r-data-table
+           r-delayedarray
+           r-delayedmatrixstats
+           r-genefilter
+           r-genomeinfodb
+           r-genomicranges
+           r-geoquery
+           r-hdf5array
+           r-illuminaio
+           r-iranges
+           r-lattice
+           r-limma
+           r-mass
+           r-mclust
+           r-nlme
+           r-nor1mix
+           r-preprocesscore
+           r-quadprog
+           r-rcolorbrewer
+           r-reshape
+           r-s4vectors
+           r-siggenes
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/hansenlab/minfi")
     (synopsis "Analyze Illumina Infinium DNA methylation arrays")
     (description
@@ -6874,36 +7283,37 @@ methylation arrays.")
 (define-public r-methylumi
   (package
     (name "r-methylumi")
-    (version "2.38.0")
+    (version "2.40.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "methylumi" version))
        (sha256
         (base32
-         "1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj"))))
+         "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
-       ("r-genefilter" ,r-genefilter)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-illuminaio" ,r-illuminaio)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-minfi" ,r-minfi)
-       ("r-reshape2" ,r-reshape2)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-annotate
+           r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-fdb-infiniummethylation-hg19
+           r-genefilter
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-illuminaio
+           r-iranges
+           r-lattice
+           r-matrixstats
+           r-minfi
+           r-reshape2
+           r-s4vectors
+           r-scales
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/methylumi")
     (synopsis "Handle Illumina methylation data")
     (description
@@ -6920,31 +7330,31 @@ and Infinium HD arrays are also included.")
 (define-public r-lumi
   (package
     (name "r-lumi")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lumi" version))
        (sha256
         (base32
-         "0qjdxjdzfnnxcm07bf51v38388s5qf1i03l1sdb9jf3gxdh8yh02"))))
+         "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-dbi" ,r-dbi)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-lattice" ,r-lattice)
-       ("r-mass" ,r-mass)
-       ("r-methylumi" ,r-methylumi)
-       ("r-mgcv" ,r-mgcv)
-       ("r-nleqslv" ,r-nleqslv)
-       ("r-preprocesscore" ,r-preprocesscore)
-       ("r-rsqlite" ,r-rsqlite)))
+     (list r-affy
+           r-annotate
+           r-annotationdbi
+           r-biobase
+           r-dbi
+           r-genomicfeatures
+           r-genomicranges
+           r-kernsmooth
+           r-lattice
+           r-mass
+           r-methylumi
+           r-mgcv
+           r-nleqslv
+           r-preprocesscore
+           r-rsqlite))
     (home-page "https://bioconductor.org/packages/lumi")
     (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
     (description
@@ -6959,37 +7369,37 @@ especially Illumina Infinium methylation microarrays.")
 (define-public r-linnorm
   (package
     (name "r-linnorm")
-    (version "2.16.0")
+    (version "2.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Linnorm" version))
        (sha256
         (base32
-         "035hrniycqadmkwg8rmzw8szv0amhy31390izy91rfrld31v2yy7"))))
+         "1bdnglznsfs1kdscqyjv595wiy09khcv9kxm4fmbnmksisqjz5qj"))))
     (properties `((upstream-name . "Linnorm")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-amap" ,r-amap)
-       ("r-apcluster" ,r-apcluster)
-       ("r-ellipse" ,r-ellipse)
-       ("r-fastcluster" ,r-fastcluster)
-       ("r-fpc" ,r-fpc)
-       ("r-ggdendro" ,r-ggdendro)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gmodels" ,r-gmodels)
-       ("r-igraph" ,r-igraph)
-       ("r-limma" ,r-limma)
-       ("r-mass" ,r-mass)
-       ("r-mclust" ,r-mclust)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rtsne" ,r-rtsne)
-       ("r-statmod" ,r-statmod)
-       ("r-vegan" ,r-vegan)
-       ("r-zoo" ,r-zoo)))
+     (list r-amap
+           r-apcluster
+           r-ellipse
+           r-fastcluster
+           r-fpc
+           r-ggdendro
+           r-ggplot2
+           r-gmodels
+           r-igraph
+           r-limma
+           r-mass
+           r-mclust
+           r-rcpp
+           r-rcpparmadillo
+           r-rtsne
+           r-statmod
+           r-vegan
+           r-zoo))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "http://www.jjwanglab.org/Linnorm/")
     (synopsis "Linear model and normality based transformation method")
     (description
@@ -7020,32 +7430,32 @@ evaluation of DEG analysis methods.")
 (define-public r-ioniser
   (package
     (name "r-ioniser")
-    (version "2.16.0")
+    (version "2.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IONiseR" version))
        (sha256
         (base32
-         "0fknlwdfd49v09zspg0337b0zzc8hqza3563yrw51viw3g35d6q3"))))
+         "1hdg446z5s616aaalzz49if1wp9nmzm2mbyva82m1vz8i7ih9m4h"))))
     (properties `((upstream-name . "IONiseR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bit64" ,r-bit64)
-       ("r-dplyr" ,r-dplyr)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-magrittr" ,r-magrittr)
-       ("r-rhdf5" ,r-rhdf5)
-       ("r-shortread" ,r-shortread)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)
-       ("r-xvector" ,r-xvector)))
+     (list r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-bit64
+           r-dplyr
+           r-ggplot2
+           r-magrittr
+           r-rhdf5
+           r-shortread
+           r-stringr
+           r-tibble
+           r-tidyr
+           r-xvector))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/IONiseR/")
     (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
     (description
@@ -7072,10 +7482,7 @@ surface of a flowcell.")
     (properties `((upstream-name . "mutoss")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-multcomp" ,r-multcomp)
-       ("r-multtest" ,r-multtest)
-       ("r-mvtnorm" ,r-mvtnorm)
-       ("r-plotrix" ,r-plotrix)))
+     (list r-multcomp r-multtest r-mvtnorm r-plotrix))
     (home-page "https://github.com/kornl/mutoss/")
     (synopsis "Unified multiple testing procedures")
     (description
@@ -7100,10 +7507,7 @@ are standardized and usable by the accompanying mutossGUI package.")
          "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-lattice" ,r-lattice)
-       ("r-mutoss" ,r-mutoss)
-       ("r-rdpack" ,r-rdpack)
-       ("r-tfisher" ,r-tfisher)))
+     (list r-lattice r-mutoss r-rdpack r-tfisher))
     (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
     (synopsis "Meta-analysis of significance values")
     (description
@@ -7117,36 +7521,37 @@ published results; and a routine for graphical display.")
 (define-public r-tradeseq
   (package
    (name "r-tradeseq")
-   (version "1.6.0")
+   (version "1.8.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "tradeSeq" version))
             (sha256
              (base32
-              "0fgmb309pvqf3chdhqgbd4lzhahcj5g71sica33nzn98qhipldx7"))))
+              "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j"))))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-biobase" ,r-biobase)
-      ("r-biocparallel" ,r-biocparallel)
-      ("r-edger" ,r-edger)
-      ("r-ggplot2" ,r-ggplot2)
-      ("r-igraph" ,r-igraph)
-      ("r-magrittr" ,r-magrittr)
-      ("r-matrix" ,r-matrix)
-      ("r-matrixstats" ,r-matrixstats)
-      ("r-mgcv" ,r-mgcv)
-      ("r-monocle" ,r-monocle)
-      ("r-pbapply" ,r-pbapply)
-      ("r-princurve" ,r-princurve)
-      ("r-rcolorbrewer" ,r-rcolorbrewer)
-      ("r-s4vectors" ,r-s4vectors)
-      ("r-singlecellexperiment" ,r-singlecellexperiment)
-      ("r-slingshot" ,r-slingshot)
-      ("r-summarizedexperiment" ,r-summarizedexperiment)
-      ("r-tibble" ,r-tibble)
-      ("r-viridis" ,r-viridis)))
+    (list r-biobase
+          r-biocparallel
+          r-edger
+          r-ggplot2
+          r-igraph
+          r-magrittr
+          r-mass
+          r-matrix
+          r-matrixstats
+          r-mgcv
+          r-pbapply
+          r-princurve
+          r-rcolorbrewer
+          r-s4vectors
+          r-singlecellexperiment
+          r-slingshot
+          r-summarizedexperiment
+          r-tibble
+          r-trajectoryutils
+          r-viridis))
    (native-inputs
-    `(("r-knitr" ,r-knitr)))
+    (list r-knitr))
    (home-page "https://statomics.github.io/tradeSeq/index.html")
    (synopsis "Trajectory-based differential expression analysis")
    (description
@@ -7173,9 +7578,7 @@ performs inference on the parameters of the GAM.")
          "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-iranges" ,r-iranges)
-       ("r-yaml" ,r-yaml)))
+     (list r-biocgenerics r-iranges r-yaml))
     (home-page "https://bioconductor.org/packages/triform/")
     (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
     (description
@@ -7187,31 +7590,31 @@ peak definition in combination with known profile characteristics.")
 (define-public r-varianttools
   (package
     (name "r-varianttools")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantTools" version))
        (sha256
         (base32
-         "1gpzrln2clfrja8rzxhsis6bi1xqglh3h2lhvqlnrx4lqxhbkv9c"))))
+         "0079dsgav4q03c4i0dhggc88iifd828n73kjv3sahim9akafdshl"))))
     (properties `((upstream-name . "VariantTools")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-bsgenome
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-matrix
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-variantannotation))
     (home-page "https://bioconductor.org/packages/VariantTools/")
     (synopsis "Tools for exploratory analysis of variant calls")
     (description
@@ -7227,18 +7630,18 @@ gmapR.")
 (define-public r-heatplus
   (package
     (name "r-heatplus")
-    (version "3.0.0")
+    (version "3.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Heatplus" version))
        (sha256
         (base32
-         "0xwg3sxmihg3p6v3nxgrqy0nrqxi6razg3b3rjh2gcb2vv8gcqng"))))
+         "0yrnjrbfn8vjzvp2742lyxdqca4s18h73j44qxw7ib95x3p4lndf"))))
     (properties `((upstream-name . "Heatplus")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-rcolorbrewer" ,r-rcolorbrewer)))
+     (list r-rcolorbrewer))
     (home-page "https://github.com/alexploner/Heatplus")
     (synopsis "Heatmaps with row and/or column covariates and colored clusters")
     (description
@@ -7252,22 +7655,20 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.18.1")
+    (version "2.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "00dbgkiv9x7g2i0anzcxpycwqqqry0y7jl3ad93lhvi31qnqq1sm"))))
+         "15qi69kkgah7g25bymk9q1xf16hp1rd040fglg0svnydylg2d0ab"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-go-db" ,r-go-db)
-       ("r-rcpp" ,r-rcpp)))
+     (list r-annotationdbi r-go-db r-rcpp))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://guangchuangyu.github.io/software/GOSemSim")
     (synopsis "GO-terms semantic similarity measures")
     (description
@@ -7281,18 +7682,17 @@ sets of GO terms, gene products and gene clusters.")
 (define-public r-anota
   (package
     (name "r-anota")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anota" version))
        (sha256
         (base32
-         "039bmcv5l44gszb6xapbihp3mfqdaaa8mfc05y702p78i7x93g5y"))))
+         "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-multtest" ,r-multtest)
-       ("r-qvalue" ,r-qvalue)))
+     (list r-multtest r-qvalue))
     (home-page "https://bioconductor.org/packages/anota/")
     (synopsis "Analysis of translational activity")
     (description
@@ -7312,14 +7712,14 @@ the data set is suitable for such analysis.")
 (define-public r-sigpathway
   (package
     (name "r-sigpathway")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "sigPathway" version))
         (sha256
           (base32
-            "1xz5nbw5dzyah8az7mpwj8m27fsvpi2jjhfg3n27dsv8rvdncqi8"))))
+            "1c46m1gbgiygcj8m65h8iwzk3fkp6nynd6rk1f5qdh7kw5ap28f9"))))
     (properties `((upstream-name . "sigPathway")))
     (build-system r-build-system)
     (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
@@ -7331,29 +7731,62 @@ specified group of genes for a pathway has a coordinated association with a
 phenotype of interest.")
     (license license:gpl2)))
 
+(define-public r-fcscan
+  (package
+    (name "r-fcscan")
+    (version "1.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "fcScan" version))
+       (sha256
+        (base32 "0b161ayq4m9xxfs0lgw632lgygzabz8gjl0n75050pa7qaazknvd"))))
+    (properties `((upstream-name . "fcScan")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-doparallel
+           r-foreach
+           r-genomicranges
+           r-iranges
+           r-plyr
+           r-rtracklayer
+           r-summarizedexperiment
+           r-variantannotation))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/fcScan")
+    (synopsis "Detect clusters of coordinates with user defined options")
+    (description
+     "This package is used to detect combination of genomic coordinates
+falling within a user defined window size along with user defined overlap
+between identified neighboring clusters.  It can be used for genomic data
+where the clusters are built on a specific chromosome or specific strand.
+Clustering can be performed with a \"greedy\" option allowing thus the
+presence of additional sites within the allowed window size.")
+    (license license:artistic2.0)))
+
 (define-public r-fgsea
   (package
     (name "r-fgsea")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fgsea" version))
        (sha256
         (base32
-         "1mhdgy46nxgv7v54bk9bqfy0vgjzl1law7zy718swdd762xn6g9d"))))
+         "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bh" ,r-bh)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-data-table" ,r-data-table)
-       ("r-fastmatch" ,r-fastmatch)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)))
+     (list r-bh
+           r-biocparallel
+           r-data-table
+           r-fastmatch
+           r-ggplot2
+           r-gridextra
+           r-matrix
+           r-rcpp))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/ctlab/fgsea/")
     (synopsis "Fast gene set enrichment analysis")
     (description
@@ -7366,27 +7799,27 @@ to multiple hypothesis correction.")
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.18.2")
+    (version "3.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "0kp6j42mpxrpd02cjrzqmrx3rvvpi90xiy4gc5km6ny3vxbhlaqw"))))
+         "10kknaqz40pb6v0fcjzp12hfpi6k5kvlqnyxx1k3y0h0wdg8hs3n"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-do-db" ,r-do-db)
-       ("r-fgsea" ,r-fgsea)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gosemsim" ,r-gosemsim)
-       ("r-qvalue" ,r-qvalue)
-       ("r-reshape2" ,r-reshape2)))
+     (list r-annotationdbi
+           r-biocparallel
+           r-do-db
+           r-fgsea
+           r-ggplot2
+           r-gosemsim
+           r-qvalue
+           r-reshape2))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://guangchuangyu.github.io/software/DOSE/")
     (synopsis "Disease ontology semantic and enrichment analysis")
     (description
@@ -7401,32 +7834,33 @@ data.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.12.2")
+    (version "1.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "194sfmcnjfi3fvvfpljg1f80f44vvvxiij336b8z1dgzki6bqa3r"))))
+         "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-cowplot" ,r-cowplot)
-       ("r-dose" ,r-dose)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggraph" ,r-ggraph)
-       ("r-ggtree" ,r-ggtree)
-       ("r-gosemsim" ,r-gosemsim)
-       ("r-igraph" ,r-igraph)
-       ("r-magrittr" ,r-magrittr)
-       ("r-plyr" ,r-plyr)
-       ("r-purrr" ,r-purrr)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-reshape2" ,r-reshape2)
-       ("r-scatterpie" ,r-scatterpie)
-       ("r-shadowtext" ,r-shadowtext)))
+     (list r-aplot
+           r-dose
+           r-ggplot2
+           r-ggraph
+           r-ggtree
+           r-gosemsim
+           r-igraph
+           r-magrittr
+           r-plyr
+           r-purrr
+           r-rcolorbrewer
+           r-reshape2
+           r-scatterpie
+           r-shadowtext
+           r-yulab-utils))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/GuangchuangYu/enrichplot")
     (synopsis "Visualization of functional enrichment result")
     (description
@@ -7438,33 +7872,33 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "4.0.5")
+    (version "4.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "1dccrl2ffhgmv3iqlmpln7z86ahpf0j9ma194fnknsgi3cd9rhrl"))))
+         "08jhcbanz24x7zdkxznxz787g0nk3jfzd7zsap13sra7qnwaswq4"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-dose" ,r-dose)
-       ("r-downloader" ,r-downloader)
-       ("r-dplyr" ,r-dplyr)
-       ("r-enrichplot" ,r-enrichplot)
-       ("r-go-db" ,r-go-db)
-       ("r-gosemsim" ,r-gosemsim)
-       ("r-magrittr" ,r-magrittr)
-       ("r-plyr" ,r-plyr)
-       ("r-qvalue" ,r-qvalue)
-       ("r-rlang" ,r-rlang)
-       ("r-tidyr" ,r-tidyr)
-       ("r-yulab-utils" ,r-yulab-utils)))
+     (list r-annotationdbi
+           r-dose
+           r-downloader
+           r-dplyr
+           r-enrichplot
+           r-go-db
+           r-gosemsim
+           r-magrittr
+           r-plyr
+           r-qvalue
+           r-rlang
+           r-tidyr
+           r-yulab-utils))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
     (synopsis "Analysis and visualization of functional profiles for gene clusters")
     (description
@@ -7475,42 +7909,42 @@ profiles (GO and KEGG) of gene and gene clusters.")
 (define-public r-clusterexperiment
   (package
     (name "r-clusterexperiment")
-    (version "2.12.0")
+    (version "2.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "clusterExperiment" version))
               (sha256
                (base32
-                "1fhmayciwn1m124b4dcs3gzbghgk9f7a7qmjnvvxc958cywcwkx5"))))
+                "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc"))))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (propagated-inputs
-     `(("r-ape" ,r-ape)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocsingular" ,r-biocsingular)
-       ("r-cluster" ,r-cluster)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-edger" ,r-edger)
-       ("r-hdf5array" ,r-hdf5array)
-       ("r-howmany" ,r-howmany)
-       ("r-kernlab" ,r-kernlab)
-       ("r-limma" ,r-limma)
-       ("r-locfdr" ,r-locfdr)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-mbkmeans" ,r-mbkmeans)
-       ("r-nmf" ,r-nmf)
-       ("r-phylobase" ,r-phylobase)
-       ("r-pracma" ,r-pracma)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rcpp" ,r-rcpp)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-stringr" ,r-stringr)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-zinbwave" ,r-zinbwave)))
+     (list r-ape
+           r-biocgenerics
+           r-biocsingular
+           r-cluster
+           r-delayedarray
+           r-edger
+           r-hdf5array
+           r-howmany
+           r-kernlab
+           r-limma
+           r-locfdr
+           r-matrix
+           r-matrixstats
+           r-mbkmeans
+           r-nmf
+           r-phylobase
+           r-pracma
+           r-rcolorbrewer
+           r-rcpp
+           r-s4vectors
+           r-scales
+           r-singlecellexperiment
+           r-stringr
+           r-summarizedexperiment
+           r-zinbwave))
     (home-page "https://bioconductor.org/packages/clusterExperiment/")
     (synopsis "Compare clusterings for single-cell sequencing")
     (description "This package provides functionality for running and comparing
@@ -7521,37 +7955,37 @@ expression data sets.")
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
-         "0ipzv7wdvfqhdyjiak956qq201igsdxm6dr6rh3dj6cssgsrnrpb"))))
+         "1nzy04fqwzb0ywiafgx3m3i2n1b0g4pcg8mlgh8yz5d3mmna4kag"))))
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-cluster" ,r-cluster)
-       ("r-fpc" ,r-fpc)
-       ("r-gbm" ,r-gbm)
-       ("r-gdata" ,r-gdata)
-       ("r-genefilter" ,r-genefilter)
-       ("r-ggvis" ,r-ggvis)
-       ("r-hwriter" ,r-hwriter)
-       ("r-magrittr" ,r-magrittr)
-       ("r-mass" ,r-mass)
-       ("r-mlbench" ,r-mlbench)
-       ("r-pls" ,r-pls)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rpart" ,r-rpart)
-       ("r-sfsmisc" ,r-sfsmisc)
-       ("r-shiny" ,r-shiny)
-       ("r-threejs" ,r-threejs)))
+     (list r-annotate
+           r-biobase
+           r-biocgenerics
+           r-cluster
+           r-fpc
+           r-gbm
+           r-gdata
+           r-genefilter
+           r-ggvis
+           r-hwriter
+           r-magrittr
+           r-mass
+           r-mlbench
+           r-pls
+           r-rcolorbrewer
+           r-rcpp
+           r-rpart
+           r-sfsmisc
+           r-shiny
+           r-threejs))
     (home-page "https://bioconductor.org/packages/MLInterfaces/")
     (synopsis "Interfaces to R machine learning procedures")
     (description
@@ -7563,14 +7997,14 @@ data in R and Bioconductor containers.")
 (define-public r-annaffy
   (package
     (name "r-annaffy")
-    (version "1.64.2")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annaffy" version))
        (sha256
         (base32
-         "03y633vgxprd2abhanj4sanmb4ymz7az5aiasxn6wjzawiqjdcb1"))))
+         "0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7580,11 +8014,7 @@ data in R and Bioconductor containers.")
              (substitute* "DESCRIPTION"
                ((", KEGG.db") "")))))))
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-dbi" ,r-dbi)
-       ("r-go-db" ,r-go-db)))
+     (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
     (home-page "https://bioconductor.org/packages/annaffy/")
     (synopsis "Annotation tools for Affymetrix biological metadata")
     (description
@@ -7599,21 +8029,20 @@ It allows searching of biological metadata using various criteria.")
 (define-public r-a4core
   (package
     (name "r-a4core")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Core" version))
        (sha256
         (base32
-         "00fi753nsayv0xspavw8r9ni1sim8ng33hp3d3kj2b8ihygd1s10"))))
+         "074aa52y6c70417lxwrclk613gbs7zv3326g9ndbbzzs5pmnh1y0"))))
     (properties `((upstream-name . "a4Core")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-glmnet" ,r-glmnet)))
+     (list r-biobase r-glmnet))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/a4Core")
     (synopsis "Automated Affymetrix array analysis core package")
     (description
@@ -7624,26 +8053,26 @@ arrays.")
 (define-public r-a4classif
   (package
     (name "r-a4classif")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Classif" version))
        (sha256
         (base32
-         "1lz85bys5dp5d1ir9c9c4wy85wkk62s14niyzzxaqrxpsji2p2iw"))))
+         "0q50d41n7drj5c9x6njyvzr6bj7glmkp1vpyz6cpj97j2v9nikwb"))))
     (properties `((upstream-name . "a4Classif")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-a4core" ,r-a4core)
-       ("r-a4preproc" ,r-a4preproc)
-       ("r-biobase" ,r-biobase)
-       ("r-glmnet" ,r-glmnet)
-       ("r-pamr" ,r-pamr)
-       ("r-rocr" ,r-rocr)
-       ("r-varselrf" ,r-varselrf)))
+     (list r-a4core
+           r-a4preproc
+           r-biobase
+           r-glmnet
+           r-pamr
+           r-rocr
+           r-varselrf))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/a4Classif/")
     (synopsis "Automated Affymetrix array analysis classification package")
     (description
@@ -7654,21 +8083,20 @@ Affymetrix arrays.")
 (define-public r-a4preproc
   (package
     (name "r-a4preproc")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Preproc" version))
        (sha256
         (base32
-         "1jibm2f5glzsrvl64hxc5sf59d4w6ry0f663p619hfr44mi1mpri"))))
+         "1qzr54w1qys1ppd71i5b57503dijfnnbn516a2mfk5l9l7wr728d"))))
     (properties `((upstream-name . "a4Preproc")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)))
+     (list r-biobase r-biocgenerics))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/a4Preproc/")
     (synopsis "Automated Affymetrix array analysis preprocessing package")
     (description
@@ -7679,20 +8107,20 @@ is used for preprocessing the arrays.")
 (define-public r-a4reporting
   (package
     (name "r-a4reporting")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Reporting" version))
        (sha256
         (base32
-         "09jjfby5znmg2fdkhpbinx2v21zrfa44qq7cylcn9ipffqx3pk86"))))
+         "1vyah71gm4ngsgy0y10cdxa9b1g810gqa5pbvb3krh5i6h35smwr"))))
     (properties `((upstream-name . "a4Reporting")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-xtable" ,r-xtable)))
+     (list r-xtable))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/a4Reporting/")
     (synopsis "Automated Affymetrix array analysis reporting package")
     (description
@@ -7703,27 +8131,27 @@ provides reporting features.")
 (define-public r-a4base
   (package
     (name "r-a4base")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Base" version))
        (sha256
         (base32
-         "101w4i0w8n7qhki22qr8l8wk8w6zalzmcywqm2g4238qv7xbnr8p"))))
+         "0rddxnflvbc6z4sj2h8js8yfh0zhrrwj8fk00wicaqp4rkr5yaxy"))))
     (properties `((upstream-name . "a4Base")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-a4core" ,r-a4core)
-       ("r-a4preproc" ,r-a4preproc)
-       ("r-annaffy" ,r-annaffy)
-       ("r-biobase" ,r-biobase)
-       ("r-genefilter" ,r-genefilter)
-       ("r-glmnet" ,r-glmnet)
-       ("r-gplots" ,r-gplots)
-       ("r-limma" ,r-limma)
-       ("r-mpm" ,r-mpm)
-       ("r-multtest" ,r-multtest)))
+     (list r-a4core
+           r-a4preproc
+           r-annaffy
+           r-biobase
+           r-genefilter
+           r-glmnet
+           r-gplots
+           r-limma
+           r-mpm
+           r-multtest))
     (home-page "https://bioconductor.org/packages/a4Base/")
     (synopsis "Automated Affymetrix array analysis base package")
     (description
@@ -7734,21 +8162,17 @@ Affymetrix arrays.")
 (define-public r-a4
   (package
     (name "r-a4")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4" version))
        (sha256
         (base32
-         "0bwn185admy5k99fkd2dhhvy7x1f75r0mqn5k24dbbg0paw6nnr8"))))
+         "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-a4base" ,r-a4base)
-       ("r-a4classif" ,r-a4classif)
-       ("r-a4core" ,r-a4core)
-       ("r-a4preproc" ,r-a4preproc)
-       ("r-a4reporting" ,r-a4reporting)))
+     (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
     (home-page "https://bioconductor.org/packages/a4/")
     (synopsis "Automated Affymetrix array analysis umbrella package")
     (description
@@ -7759,39 +8183,39 @@ Affymetrix arrays.")
 (define-public r-abseqr
   (package
     (name "r-abseqr")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "abseqR" version))
        (sha256
         (base32
-         "1xvk84gd1lfq1icrfwwd6y79zywrisfnc3knprigzzax31aks32c"))))
+         "1v9g71x689ly107c0qmc5iv8qk63nn6lp7yd03jf7hlcafmvqsvz"))))
     (properties `((upstream-name . "abseqR")))
     (build-system r-build-system)
     (inputs
-     `(("pandoc" ,pandoc)))
+     (list pandoc))
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-biocstyle" ,r-biocstyle)
-       ("r-circlize" ,r-circlize)
-       ("r-flexdashboard" ,r-flexdashboard)
-       ("r-ggcorrplot" ,r-ggcorrplot)
-       ("r-ggdendro" ,r-ggdendro)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-knitr" ,r-knitr)
-       ("r-plotly" ,r-plotly)
-       ("r-plyr" ,r-plyr)
-       ("r-png" ,r-png)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("r-stringr" ,r-stringr)
-       ("r-vegan" ,r-vegan)
-       ("r-venndiagram" ,r-venndiagram)))
+     (list r-biocparallel
+           r-biocstyle
+           r-circlize
+           r-flexdashboard
+           r-ggcorrplot
+           r-ggdendro
+           r-ggplot2
+           r-gridextra
+           r-knitr
+           r-plotly
+           r-plyr
+           r-png
+           r-rcolorbrewer
+           r-reshape2
+           r-rmarkdown
+           r-stringr
+           r-vegan
+           r-venndiagram))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/malhamdoosh/abseqR")
     (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
     (description
@@ -7807,21 +8231,19 @@ further downstream analysis on its output.")
 (define-public r-bacon
   (package
     (name "r-bacon")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bacon" version))
        (sha256
         (base32
-         "1yp0675n1g8rxdjdd7w8al5c9jq96h0kfm8218mc50z0p2fasgbj"))))
+         "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-ellipse" ,r-ellipse)
-       ("r-ggplot2" ,r-ggplot2)))
+     (list r-biocparallel r-ellipse r-ggplot2))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/bacon/")
     (synopsis "Controlling bias and inflation in association studies")
     (description
@@ -7834,22 +8256,18 @@ fitting a three-component normal mixture on z-scores.")
 (define-public r-rgadem
   (package
     (name "r-rgadem")
-    (version "2.40.0")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32
-         "05drbhjqn5kik6k4h03vr3d2b6pv5rm65lsnkyx4caxxcdii4jzm"))))
+         "1v8xgqqv7m2kyc38x9ppwsv87ivll5ppd6z76zcxj5yspkkrqw3v"))))
     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-seqlogo" ,r-seqlogo)))
+     (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
     (home-page "https://bioconductor.org/packages/rGADEM/")
     (synopsis "De novo sequence motif discovery")
     (description
@@ -7871,15 +8289,15 @@ genomic sequence data.")
     (properties `((upstream-name . "MotIV")))
     (build-system r-build-system)
     (inputs
-     `(("gsl" ,gsl)))
+     (list gsl))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-rgadem" ,r-rgadem)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocgenerics
+           r-biostrings
+           r-genomicranges
+           r-iranges
+           r-lattice
+           r-rgadem
+           r-s4vectors))
     (home-page "https://bioconductor.org/packages/MotIV/")
     (synopsis "Motif identification and validation")
     (description
@@ -7892,24 +8310,24 @@ distributions, modules and filter motifs.")
 (define-public r-motifdb
   (package
    (name "r-motifdb")
-   (version "1.34.0")
+   (version "1.36.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MotifDb" version))
             (sha256
-             (base32 "04cmgg5mw1cqbg95zyfc2imykmdxyff16w26rq97xghcxwiq2b3z"))))
+             (base32 "0a2zg26zzk7bj5c33mbwl8dx9lh1hns8q8kwp09rbfjdichv7425"))))
    (properties `((upstream-name . "MotifDb")))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-biocgenerics" ,r-biocgenerics)
-      ("r-biostrings" ,r-biostrings)
-      ("r-genomicranges" ,r-genomicranges)
-      ("r-iranges" ,r-iranges)
-      ("r-rtracklayer" ,r-rtracklayer)
-      ("r-s4vectors" ,r-s4vectors)
-      ("r-splitstackshape" ,r-splitstackshape)))
+    (list r-biocgenerics
+          r-biostrings
+          r-genomicranges
+          r-iranges
+          r-rtracklayer
+          r-s4vectors
+          r-splitstackshape))
    (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
    (home-page "https://www.bioconductor.org/packages/MotifDb/")
    (synopsis "Annotated collection of protein-DNA binding sequence motifs")
    (description "This package provides more than 2000 annotated position
@@ -7919,35 +8337,35 @@ frequency matrices from nine public sources, for multiple organisms.")
 (define-public r-motifbreakr
   (package
    (name "r-motifbreakr")
-   (version "2.6.1")
+   (version "2.8.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "motifbreakR" version))
             (sha256
-             (base32 "1n6v8a7c27aswmbrlcwcpghf27aplkc6nn923imglc3c0sh2lkrz"))))
+             (base32 "0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj"))))
    (properties `((upstream-name . "motifbreakR")))
    (build-system r-build-system)
    (propagated-inputs
-    `(("r-biocgenerics" ,r-biocgenerics)
-      ("r-biocparallel" ,r-biocparallel)
-      ("r-biostrings" ,r-biostrings)
-      ("r-bsgenome" ,r-bsgenome)
-      ("r-genomeinfodb" ,r-genomeinfodb)
-      ("r-genomicranges" ,r-genomicranges)
-      ("r-grimport" ,r-grimport)
-      ("r-gviz" ,r-gviz)
-      ("r-iranges" ,r-iranges)
-      ("r-matrixstats" ,r-matrixstats)
-      ("r-motifdb" ,r-motifdb)
-      ("r-motifstack" ,r-motifstack)
-      ("r-rtracklayer" ,r-rtracklayer)
-      ("r-s4vectors" ,r-s4vectors)
-      ("r-stringr" ,r-stringr)
-      ("r-summarizedexperiment" ,r-summarizedexperiment)
-      ("r-tfmpvalue" ,r-tfmpvalue)
-      ("r-variantannotation" ,r-variantannotation)))
+    (list r-biocgenerics
+          r-biocparallel
+          r-biostrings
+          r-bsgenome
+          r-genomeinfodb
+          r-genomicranges
+          r-grimport
+          r-gviz
+          r-iranges
+          r-matrixstats
+          r-motifdb
+          r-motifstack
+          r-rtracklayer
+          r-s4vectors
+          r-stringr
+          r-summarizedexperiment
+          r-tfmpvalue
+          r-variantannotation))
    (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
    (home-page "https://www.bioconductor.org/packages/motifbreakR/")
    (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
    (description "This package allows biologists to judge in the first place
@@ -7970,24 +8388,20 @@ Bioconductor.")
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifStack" version))
        (sha256
         (base32
-         "0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp"))))
+         "1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz"))))
     (properties `((upstream-name . "motifStack")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-ade4" ,r-ade4)
-       ("r-biostrings" ,r-biostrings)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-htmlwidgets" ,r-htmlwidgets)
-       ("r-xml" ,r-xml)))
+     (list r-ade4 r-biostrings r-ggplot2 r-htmlwidgets r-xml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/motifStack/")
     (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
     (description
@@ -8001,33 +8415,33 @@ type and symbol colors.")
 (define-public r-genomicscores
   (package
     (name "r-genomicscores")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicScores" version))
        (sha256
         (base32
-         "1b8982fj0r7igj749wljsdfn3c985w8n3d5gbhr5rw73llfb8x6w"))))
+         "18fzi2qi95851ci7qrzwpb7v6fhwp6xi1d1vk11xbygpbvql5mls"))))
     (properties `((upstream-name . "GenomicScores")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationhub" ,r-annotationhub)
-       ("r-biobase" ,r-biobase)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biostrings" ,r-biostrings)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-hdf5array" ,r-hdf5array)
-       ("r-iranges" ,r-iranges)
-       ("r-rhdf5" ,r-rhdf5)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xml" ,r-xml)))
+     (list r-annotationhub
+           r-biobase
+           r-biocfilecache
+           r-biocgenerics
+           r-biocmanager
+           r-biostrings
+           r-delayedarray
+           r-genomeinfodb
+           r-genomicranges
+           r-hdf5array
+           r-iranges
+           r-rhdf5
+           r-s4vectors
+           r-xml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/rcastelo/GenomicScores/")
     (synopsis "Work with genome-wide position-specific scores")
     (description
@@ -8038,37 +8452,37 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "168g3xkhjzrfjpa1ynifdyfhsxx3rpyrbybsarlzr9kslw1cdkxl"))))
+         "0i1i3bfkp1xsjdl1nd56mlh66qz3aasd1hp09d4i31njz2f9znwn"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-chippeakanno" ,r-chippeakanno)
-       ("r-edger" ,r-edger)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-genomicscores" ,r-genomicscores)
-       ("r-iranges" ,r-iranges)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-limma" ,r-limma)
-       ("r-motifstack" ,r-motifstack)
-       ("r-preseqr" ,r-preseqr)
-       ("r-randomforest" ,r-randomforest)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocgenerics
+           r-biostrings
+           r-bsgenome
+           r-chippeakanno
+           r-edger
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-genomicscores
+           r-iranges
+           r-kernsmooth
+           r-limma
+           r-motifstack
+           r-preseqr
+           r-randomforest
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/ATACseqQC/")
     (synopsis "ATAC-seq quality control")
     (description
@@ -8085,26 +8499,26 @@ footprints.")
 (define-public r-gofuncr
   (package
     (name "r-gofuncr")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOfuncR" version))
        (sha256
         (base32
-         "0lp2gmjlsk1yqxim5pi26i27iijw11lrcxmji7ynlag359yfnynd"))))
+         "08n1d03i4l2dl47axmrziiypi83yffndf0ww1b32skyjm2r0x127"))))
     (properties `((upstream-name . "GOfuncR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gtools" ,r-gtools)
-       ("r-iranges" ,r-iranges)
-       ("r-mapplots" ,r-mapplots)
-       ("r-rcpp" ,r-rcpp)
-       ("r-vioplot" ,r-vioplot)))
+     (list r-annotationdbi
+           r-genomicranges
+           r-gtools
+           r-iranges
+           r-mapplots
+           r-rcpp
+           r-vioplot))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/GOfuncR/")
     (synopsis "Gene ontology enrichment using FUNC")
     (description
@@ -8134,25 +8548,25 @@ annotations and ontologies.")
 (define-public r-abaenrichment
   (package
     (name "r-abaenrichment")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ABAEnrichment" version))
        (sha256
         (base32
-         "15v5n6d3mnj9d86swkh9agfvrsd065dldaywm1adwmkhhk525wmd"))))
+         "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
     (properties `((upstream-name . "ABAEnrichment")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-abadata" ,r-abadata)
-       ("r-data-table" ,r-data-table)
-       ("r-gofuncr" ,r-gofuncr)
-       ("r-gplots" ,r-gplots)
-       ("r-gtools" ,r-gtools)
-       ("r-rcpp" ,r-rcpp)))
+     (list r-abadata
+           r-data-table
+           r-gofuncr
+           r-gplots
+           r-gtools
+           r-rcpp))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/ABAEnrichment/")
     (synopsis "Gene expression enrichment in human brain regions")
     (description
@@ -8178,8 +8592,7 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.")
      `((upstream-name . "AnnotationFuncs")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-dbi" ,r-dbi)))
+     (list r-annotationdbi r-dbi))
     (home-page "https://www.iysik.com/r/annotationfuncs")
     (synopsis "Annotation translation functions")
     (description
@@ -8191,18 +8604,18 @@ different identifieres using the Biocore Data Team data-packages (e.g.
 (define-public r-annotationtools
   (package
     (name "r-annotationtools")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotationTools" version))
        (sha256
         (base32
-         "18dd8saqx17fplvv5sbfz4p9fy7ksy3n9348rd3qlczihcrh9i3w"))))
+         "0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh"))))
     (properties
      `((upstream-name . "annotationTools")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-biobase" ,r-biobase)))
+    (propagated-inputs (list r-biobase))
     (home-page "https://bioconductor.org/packages/annotationTools/")
     (synopsis "Annotate microarrays and perform gene expression analyses")
     (description
@@ -8216,39 +8629,39 @@ text files).")
 (define-public r-allelicimbalance
   (package
     (name "r-allelicimbalance")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AllelicImbalance" version))
        (sha256
         (base32
-         "1mn6975npncmfjlpjs3s2pgsrm32xgvnyl2vh1922l6vra97dkrc"))))
+         "1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq"))))
     (properties
      `((upstream-name . "AllelicImbalance")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gridextra" ,r-gridextra)
-       ("r-gviz" ,r-gviz)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-latticeextra" ,r-latticeextra)
-       ("r-nlme" ,r-nlme)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-seqinr" ,r-seqinr)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-annotationdbi
+           r-biocgenerics
+           r-biostrings
+           r-bsgenome
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-gridextra
+           r-gviz
+           r-iranges
+           r-lattice
+           r-latticeextra
+           r-nlme
+           r-rsamtools
+           r-s4vectors
+           r-seqinr
+           r-summarizedexperiment
+           r-variantannotation))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/pappewaio/AllelicImbalance")
     (synopsis "Investigate allele-specific expression")
     (description
@@ -8259,27 +8672,27 @@ investigation using RNA-seq data.")
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "0qdac3qalcki20r90k40cc8d0lfywzn9pffg9d719yvs7nrsfdjr"))))
+         "1lclf8hkhrm6g5fp8yhvjxnwgf8p0j9ffxsmcybz4rjvmwkiz5dp"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-data-table" ,r-data-table)
-       ("r-gseabase" ,r-gseabase)
-       ("r-mixtools" ,r-mixtools)
-       ("r-r-utils" ,r-r-utils)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-biocgenerics
+           r-data-table
+           r-gseabase
+           r-mixtools
+           r-r-utils
+           r-s4vectors
+           r-shiny
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/AUCell/")
     (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
     (description
@@ -8298,29 +8711,29 @@ needed.")
 (define-public r-ebimage
   (package
     (name "r-ebimage")
-    (version "4.34.0")
+    (version "4.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBImage" version))
        (sha256
         (base32
-         "1z3cxxg593d66nczz5hh2hdj1d87wc0lxrzc5sn6bp43n351q8h3"))))
+         "030vpn55ppfqq4408c4db4w40d17x1yq6zajb11p2glikvm1q619"))))
     (properties `((upstream-name . "EBImage")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-abind" ,r-abind)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-fftwtools" ,r-fftwtools)
-       ("r-htmltools" ,r-htmltools)
-       ("r-htmlwidgets" ,r-htmlwidgets)
-       ("r-jpeg" ,r-jpeg)
-       ("r-locfit" ,r-locfit)
-       ("r-png" ,r-png)
-       ("r-rcurl" ,r-rcurl)
-       ("r-tiff" ,r-tiff)))
+     (list r-abind
+           r-biocgenerics
+           r-fftwtools
+           r-htmltools
+           r-htmlwidgets
+           r-jpeg
+           r-locfit
+           r-png
+           r-rcurl
+           r-tiff))
     (native-inputs
-     `(("r-knitr" ,r-knitr))) ; for vignettes
+     (list r-knitr)) ; for vignettes
     (home-page "https://github.com/aoles/EBImage")
     (synopsis "Image processing and analysis toolbox for R")
     (description
@@ -8337,28 +8750,27 @@ visualization with image data.")
 (define-public r-yamss
   (package
     (name "r-yamss")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yamss" version))
        (sha256
         (base32
-         "1al615x778h17jqiyhiyf6djaq9iygs1hlbrna6y4xc0f2kvgxld"))))
+         "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-data-table" ,r-data-table)
-       ("r-ebimage" ,r-ebimage)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-matrix" ,r-matrix)
-       ("r-mzr" ,r-mzr)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment"
-        ,r-summarizedexperiment)))
+     (list r-biocgenerics
+           r-data-table
+           r-ebimage
+           r-iranges
+           r-limma
+           r-matrix
+           r-mzr
+           r-s4vectors
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/hansenlab/yamss")
     (synopsis "Tools for high-throughput metabolomics")
     (description
@@ -8371,22 +8783,19 @@ analysis.")
 (define-public r-gtrellis
   (package
     (name "r-gtrellis")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gtrellis" version))
        (sha256
         (base32
-         "0l5271cpzjlm4m0v6xcdg2vxlbhn53x1fd59ynb9jwll93av5h1f"))))
+         "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-circlize" ,r-circlize)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-getoptlong" ,r-getoptlong)
-       ("r-iranges" ,r-iranges)))
+     (list r-circlize r-genomicranges r-getoptlong r-iranges))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/jokergoo/gtrellis")
     (synopsis "Genome level Trellis layout")
     (description
@@ -8400,33 +8809,33 @@ genomic categories and to add self-defined graphics in the plot.")
 (define-public r-somaticsignatures
   (package
     (name "r-somaticsignatures")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SomaticSignatures" version))
        (sha256
         (base32
-         "0jr11c9hz7m49xc8pi6xrr5fhbv68vafvqpzhr0pmm51vvr1vfs9"))))
+         "1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql"))))
     (properties
      `((upstream-name . "SomaticSignatures")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggbio" ,r-ggbio)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-nmf" ,r-nmf)
-       ("r-pcamethods" ,r-pcamethods)
-       ("r-proxy" ,r-proxy)
-       ("r-reshape2" ,r-reshape2)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-biobase
+           r-biostrings
+           r-genomeinfodb
+           r-genomicranges
+           r-ggbio
+           r-ggplot2
+           r-iranges
+           r-nmf
+           r-pcamethods
+           r-proxy
+           r-reshape2
+           r-s4vectors
+           r-variantannotation))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/juliangehring/SomaticSignatures")
     (synopsis "Somatic signatures")
     (description
@@ -8439,42 +8848,42 @@ decomposition algorithms.")
 (define-public r-yapsa
   (package
     (name "r-yapsa")
-    (version "1.18.0")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "YAPSA" version))
        (sha256
         (base32
-         "1xfkgjlm0rxz82qcaqzx95cwirxifd9dsswjg3zcqmz03v7a0gz2"))))
+         "08r05fzpraggbxv15lx0b68kjlkysp0rcdlm6n9avzmlsdqplb2h"))))
     (properties `((upstream-name . "YAPSA")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-circlize" ,r-circlize)
-       ("r-complexheatmap" ,r-complexheatmap)
-       ("r-corrplot" ,r-corrplot)
-       ("r-dendextend" ,r-dendextend)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-getoptlong" ,r-getoptlong)
-       ("r-ggbeeswarm" ,r-ggbeeswarm)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-gtrellis" ,r-gtrellis)
-       ("r-keggrest" ,r-keggrest)
-       ("r-limsolve" ,r-limsolve)
-       ("r-magrittr" ,r-magrittr)
-       ("r-pmcmr" ,r-pmcmr)
-       ("r-pracma" ,r-pracma)
-       ("r-reshape2" ,r-reshape2)
-       ("r-somaticsignatures" ,r-somaticsignatures)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-biostrings
+           r-bsgenome-hsapiens-ucsc-hg19
+           r-circlize
+           r-complexheatmap
+           r-corrplot
+           r-dendextend
+           r-doparallel
+           r-dplyr
+           r-genomeinfodb
+           r-genomicranges
+           r-getoptlong
+           r-ggbeeswarm
+           r-ggplot2
+           r-gridextra
+           r-gtrellis
+           r-keggrest
+           r-limsolve
+           r-magrittr
+           r-pmcmrplus
+           r-pracma
+           r-reshape2
+           r-somaticsignatures
+           r-variantannotation))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/YAPSA/")
     (synopsis "Yet another package for signature analysis")
     (description
@@ -8488,22 +8897,22 @@ provided.")
 (define-public r-gcrma
   (package
     (name "r-gcrma")
-    (version "2.64.0")
+    (version "2.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gcrma" version))
        (sha256
         (base32
-         "1z4abw9s2hs3csnx25nli7fpvb3rh3l0swzl0wfqp087fcs78pxi"))))
+         "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-affyio" ,r-affyio)
-       ("r-biobase" ,r-biobase)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biostrings" ,r-biostrings)
-       ("r-xvector" ,r-xvector)))
+     (list r-affy
+           r-affyio
+           r-biobase
+           r-biocmanager
+           r-biostrings
+           r-xvector))
     (home-page "https://bioconductor.org/packages/gcrma/")
     (synopsis "Background adjustment using sequence information")
     (description
@@ -8534,11 +8943,7 @@ gene-specific binding is expected.")
          "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-gcrma" ,r-gcrma)
-       ("r-genefilter" ,r-genefilter)))
+     (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
     (home-page "https://bioconductor.org/packages/simpleaffy/")
     (synopsis "Very simple high level analysis of Affymetrix data")
     (description
@@ -8562,7 +8967,7 @@ generating high resolution journal figures.")
          "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-simpleaffy" ,r-simpleaffy)))
+     (list r-simpleaffy))
     (home-page "https://bioconductor.org/packages/yaqcaffy/")
     (synopsis "Affymetrix quality control and reproducibility analysis")
     (description
@@ -8574,25 +8979,25 @@ chips with the MAQC reference datasets.")
 (define-public r-quantro
   (package
     (name "r-quantro")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "quantro" version))
        (sha256
         (base32
-         "1fkma2ic448h2lrlza8ipg65gpfsz4fhlxcnjpmzhhmzp2xi2p4a"))))
+         "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-doparallel" ,r-doparallel)
-       ("r-foreach" ,r-foreach)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iterators" ,r-iterators)
-       ("r-minfi" ,r-minfi)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+     (list r-biobase
+           r-doparallel
+           r-foreach
+           r-ggplot2
+           r-iterators
+           r-minfi
+           r-rcolorbrewer))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/quantro/")
     (synopsis "Test for when to use quantile normalization")
     (description
@@ -8607,29 +9012,29 @@ groups.")
 (define-public r-yarn
   (package
     (name "r-yarn")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yarn" version))
        (sha256
         (base32
-         "1x07l255x52z6cgdc2j8285shqszhr034xm5686rp6d35vah55ji"))))
+         "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biomart" ,r-biomart)
-       ("r-downloader" ,r-downloader)
-       ("r-edger" ,r-edger)
-       ("r-gplots" ,r-gplots)
-       ("r-limma" ,r-limma)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-preprocesscore" ,r-preprocesscore)
-       ("r-quantro" ,r-quantro)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-readr" ,r-readr)))
+     (list r-biobase
+           r-biomart
+           r-downloader
+           r-edger
+           r-gplots
+           r-limma
+           r-matrixstats
+           r-preprocesscore
+           r-quantro
+           r-rcolorbrewer
+           r-readr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/yarn/")
     (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
     (description
@@ -8644,24 +9049,24 @@ large RNA-seq experiments.")
 (define-public r-roar
   (package
     (name "r-roar")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "roar" version))
        (sha256
         (base32
-         "0vp0n90rvjm8rzwkbrxa3fasb9val56bz2srz72xwsl3jzb5yk6w"))))
+         "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-biocgenerics
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-iranges
+           r-rtracklayer
+           r-s4vectors
+           r-summarizedexperiment))
     (home-page "https://github.com/vodkatad/roar/")
     (synopsis "Identify differential APA usage from RNA-seq alignments")
     (description
@@ -8684,17 +9089,17 @@ sites and alignments obtained from standard RNA-seq experiments.")
     (properties `((upstream-name . "XBSeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-deseq2" ,r-deseq2)
-       ("r-dplyr" ,r-dplyr)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-locfit" ,r-locfit)
-       ("r-magrittr" ,r-magrittr)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-pracma" ,r-pracma)
-       ("r-roar" ,r-roar)))
+     (list r-biobase
+           r-deseq2
+           r-dplyr
+           r-ggplot2
+           r-locfit
+           r-magrittr
+           r-matrixstats
+           r-pracma
+           r-roar))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/Liuy12/XBSeq")
     (synopsis "Test for differential expression for RNA-seq data")
     (description
@@ -8712,19 +9117,19 @@ genes.")
 (define-public r-massspecwavelet
   (package
     (name "r-massspecwavelet")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MassSpecWavelet" version))
        (sha256
         (base32
-         "1cs32sig1yvqn9xs0cvhfpmkh2lbllx7aab80sz58x03wnx8v60z"))))
+         "1icqyxkx5a9y3wahkxpxngw85c7l4hih1ym9nwwn9qy93pnw1zi4"))))
     (properties
      `((upstream-name . "MassSpecWavelet")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-waveslim" ,r-waveslim)))
+     (list r-waveslim))
     (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
     (synopsis "Mass spectrum processing by wavelet-based algorithms")
     (description
@@ -8736,34 +9141,35 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.14.1")
+    (version "3.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "1g8k90p0sbcb3rdrbldj5bcjp2piy5ldni4jplyr78vjpmrmvqk7"))))
+         "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-massspecwavelet" ,r-massspecwavelet)
-       ("r-mscoreutils" ,r-mscoreutils)
-       ("r-msnbase" ,r-msnbase)
-       ("r-mzr" ,r-mzr)
-       ("r-plyr" ,r-plyr)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rann" ,r-rann)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-robustbase" ,r-robustbase)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-iranges
+           r-lattice
+           r-massspecwavelet
+           r-mscoreutils
+           r-msfeatures
+           r-msnbase
+           r-mzr
+           r-plyr
+           r-protgenerics
+           r-rann
+           r-rcolorbrewer
+           r-robustbase
+           r-s4vectors
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/xcms/")
     (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
     (description
@@ -8776,22 +9182,20 @@ data for high-throughput, untargeted analyte profiling.")
 (define-public r-wrench
   (package
     (name "r-wrench")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Wrench" version))
        (sha256
         (base32
-         "0yssmqayaryrc0asjjqxdipqdfg309llrzldx38jrfgdsza6bvs0"))))
+         "1vzv7sswijgb8nq58yrc19wlw2nnpjvans86fqqzs4p8wvq8j06n"))))
     (properties `((upstream-name . "Wrench")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-limma" ,r-limma)
-       ("r-locfit" ,r-locfit)
-       ("r-matrixstats" ,r-matrixstats)))
+     (list r-limma r-locfit r-matrixstats))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/HCBravoLab/Wrench")
     (synopsis "Wrench normalization for sparse count data")
     (description
@@ -8802,28 +9206,28 @@ that arising from 16s metagenomic surveys.")
 (define-public r-wiggleplotr
   (package
     (name "r-wiggleplotr")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wiggleplotr" version))
        (sha256
         (base32
-         "13f3g6fcc29k0g21mhnypm3nc6qqjw867vamvfkdzynspsfb32ga"))))
+         "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-assertthat" ,r-assertthat)
-       ("r-cowplot" ,r-cowplot)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-purrr" ,r-purrr)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-assertthat
+           r-cowplot
+           r-dplyr
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-purrr
+           r-rtracklayer
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/wiggleplotr/")
     (synopsis "Make read coverage plots from BigWig files")
     (description
@@ -8836,14 +9240,14 @@ visualization of exonic read coverage.")
 (define-public r-widgettools
   (package
     (name "r-widgettools")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "widgetTools" version))
        (sha256
         (base32
-         "186xgpgyfyi4angxhz6558lfpzvvszzlpyfr8xnbccs3gshk3db2"))))
+         "0jajfh78116wjfwbmzfvcbxswai4jj9ypzmfhs5j5iypaf8zff8j"))))
     (properties `((upstream-name . "widgetTools")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/widgetTools/")
@@ -8857,27 +9261,26 @@ widgets in R.")
 (define-public r-webbioc
   (package
     (name "r-webbioc")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "webbioc" version))
        (sha256
         (base32
-         "1mpdw477j78s2nvlf2lzm6mdjcpamyyazjn060h9q3apawn6zajx"))))
+         "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17"))))
     (build-system r-build-system)
     (inputs
-     `(("netpbm" ,netpbm)
-       ("perl" ,perl)))
+     (list netpbm perl))
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-annaffy" ,r-annaffy)
-       ("r-biobase" ,r-biobase)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-gcrma" ,r-gcrma)
-       ("r-multtest" ,r-multtest)
-       ("r-qvalue" ,r-qvalue)
-       ("r-vsn" ,r-vsn)))
+     (list r-affy
+           r-annaffy
+           r-biobase
+           r-biocmanager
+           r-gcrma
+           r-multtest
+           r-qvalue
+           r-vsn))
     (home-page "https://www.bioconductor.org/")
     (synopsis "Bioconductor web interface")
     (description
@@ -8890,25 +9293,25 @@ Currently only Affymetrix oligonucleotide analysis is supported.")
 (define-public r-zinbwave
   (package
     (name "r-zinbwave")
-    (version "1.14.2")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zinbwave" version))
        (sha256
         (base32
-         "1y8krazz2qdn0wn8ijjs2gn5dl5l960v6bijbkvh0r8066l7viky"))))
+         "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-edger" ,r-edger)
-       ("r-genefilter" ,r-genefilter)
-       ("r-matrix" ,r-matrix)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-softimpute" ,r-softimpute)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-biocparallel
+           r-edger
+           r-genefilter
+           r-matrix
+           r-singlecellexperiment
+           r-softimpute
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/zinbwave")
     (synopsis "Zero-inflated negative binomial model for RNA-seq data")
     (description "This package implements a general and flexible zero-inflated
@@ -8923,24 +9326,20 @@ the data.")
 (define-public r-zfpkm
   (package
     (name "r-zfpkm")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zFPKM" version))
        (sha256
         (base32
-         "1k7xaxr2gn26y8bps5l32g2axfhdn07nbk4q3qcx32d5jm75qkx2"))))
+         "0fk05vrmyyrhmkwi06lsi553mlpqj3fgwhk1kygz83iqv5z2vfw9"))))
     (properties `((upstream-name . "zFPKM")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-checkmate" ,r-checkmate)
-       ("r-dplyr" ,r-dplyr)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-tidyr" ,r-tidyr)))
+     (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/ronammar/zFPKM/")
     (synopsis "Functions to facilitate zFPKM transformations")
     (description
@@ -8952,20 +9351,22 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
 (define-public r-rbowtie2
   (package
     (name "r-rbowtie2")
-    (version "1.14.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie2" version))
        (sha256
         (base32
-         "0r5yqjal48xlcv5cidi7p3zwygvsllmv2zzkwkc9kfq083l2i4ih"))))
+         "0xpvrx2ak9x913sym4l46ycwbnmpcdwb3bf3dfd2gsp0krv8vh1x"))))
     (properties `((upstream-name . "Rbowtie2")))
     (build-system r-build-system)
+    (propagated-inputs
+     (list r-magrittr r-rsamtools))
     (inputs
-     `(("zlib" ,zlib)))
+     (list samtools zlib))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/Rbowtie2/")
     (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
     (description
@@ -8977,24 +9378,24 @@ rapid adapter trimming, identification, and read merging.")
 (define-public r-progeny
   (package
     (name "r-progeny")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "progeny" version))
        (sha256
         (base32
-         "10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8"))))
+         "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-dplyr" ,r-dplyr)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-gridextra" ,r-gridextra)
-       ("r-tidyr" ,r-tidyr)))
+     (list r-biobase
+           r-dplyr
+           r-ggplot2
+           r-ggrepel
+           r-gridextra
+           r-tidyr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/saezlab/progeny")
     (synopsis "Pathway responsive gene activity inference")
     (description
@@ -9007,18 +9408,18 @@ expression\".")
 (define-public r-arrmnormalization
   (package
     (name "r-arrmnormalization")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ARRmNormalization" version))
        (sha256
         (base32
-         "0ni3vblcadhwxaq1pf1n9jn66cp3bqch68ww4c8zh19zagil2y7r"))))
+         "1ryqr3mpakjml0jhbk28k2z511sdl87wxdczxq1rwx98s0pc9mnh"))))
     (properties
      `((upstream-name . "ARRmNormalization")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
+    (propagated-inputs (list r-arrmdata))
     (home-page "https://bioconductor.org/packages/ARRmNormalization/")
     (synopsis "Adaptive robust regression normalization for methylation data")
     (description
@@ -9030,27 +9431,27 @@ Infinium HumanMethylation 450k assay.")
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "0ymg4hmabk233qgassld62achjylm12rnidxbakfkx4dvvlbhxxv"))))
+         "11qayqmgv274hc4h1v222sma07wkxjm8002fl6w3yvi225zq1qc1"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-curl" ,r-curl)
-       ("r-dbi" ,r-dbi)
-       ("r-dbplyr" ,r-dbplyr)
-       ("r-dplyr" ,r-dplyr)
-       ("r-filelock" ,r-filelock)
-       ("r-httr" ,r-httr)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-rsqlite" ,r-rsqlite)))
+     (list r-curl
+           r-dbi
+           r-dbplyr
+           r-dplyr
+           r-filelock
+           r-httr
+           r-rappdirs
+           r-rsqlite))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiocFileCache/")
     (synopsis "Manage files across sessions")
     (description
@@ -9063,17 +9464,17 @@ and data files used across sessions.")
 (define-public r-iclusterplus
   (package
     (name "r-iclusterplus")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iClusterPlus" version))
        (sha256
         (base32
-         "1haj25c4cmmjjvh181b41a9pvkh92f7k2w4ljn17iqg31vm45za1"))))
+         "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b"))))
     (properties `((upstream-name . "iClusterPlus")))
     (build-system r-build-system)
-    (native-inputs `(("gfortran" ,gfortran)))
+    (native-inputs (list gfortran))
     (home-page "https://bioconductor.org/packages/iClusterPlus/")
     (synopsis "Integrative clustering of multi-type genomic data")
     (description
@@ -9093,20 +9494,19 @@ Gaussian distributions.")
 (define-public r-rbowtie
   (package
     (name "r-rbowtie")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie" version))
        (sha256
         (base32
-         "0mfikbrs28q7r3lnsq0jma5x6nkrnm3q46242jh35w9c969jk5yy"))))
+         "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr"))))
     (properties `((upstream-name . "Rbowtie")))
     (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
+    (inputs (list zlib))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/Rbowtie/")
     (synopsis "R bowtie wrapper")
     (description
@@ -9118,33 +9518,33 @@ alignment tool.")
 (define-public r-sgseq
   (package
     (name "r-sgseq")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SGSeq" version))
        (sha256
         (base32
-         "0i1yaw8h8gibakvaf1xd6nnjx2bsb2s9c0q74rbq9lm7haihivp6"))))
+         "15l0r6svs27k82dd472is26shwayz6rs5ylg5gpf3mldr7sa5kja"))))
     (properties `((upstream-name . "SGSeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-igraph" ,r-igraph)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-runit" ,r-runit)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-annotationdbi
+           r-biocgenerics
+           r-biostrings
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-igraph
+           r-iranges
+           r-rsamtools
+           r-rtracklayer
+           r-runit
+           r-s4vectors
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/SGSeq/")
     (synopsis "Splice event prediction and quantification from RNA-seq data")
     (description
@@ -9161,14 +9561,14 @@ interpretation.")
 (define-public r-rhisat2
   (package
     (name "r-rhisat2")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhisat2" version))
        (sha256
         (base32
-         "1hqahh5h22mj2crqp6r9xnm111xmfgk39c100rcaziqrpdy5npk8"))))
+         "092rws9vjxgm2jpkbp6ign47zmillyyidnc7ylcbn4zr9j5lwv0y"))))
     (properties `((upstream-name . "Rhisat2")))
     (build-system r-build-system)
     (arguments
@@ -9184,11 +9584,9 @@ interpretation.")
                (("^CPP =.*") (which "g++")))
              #t)))))
     (propagated-inputs
-     `(("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-sgseq" ,r-sgseq)))
+     (list r-genomicfeatures r-genomicranges r-sgseq))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/fmicompbio/Rhisat2")
     (synopsis "R Wrapper for HISAT2 sequence aligner")
     (description
@@ -9201,37 +9599,36 @@ index.")
 (define-public r-quasr
   (package
     (name "r-quasr")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "QuasR" version))
        (sha256
         (base32
-         "1635ff11ahzjrh3cdcxrq5bgd100n444k7mc0maz0jx21vj8qqb1"))))
+         "0d292xgaq8d3cdpa9anabda03lis46xc29iw9c5k5i3sj7dcr4g5"))))
     (properties `((upstream-name . "QuasR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rbowtie" ,r-rbowtie)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shortread" ,r-shortread)))
+     (list r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-bsgenome
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicfiles
+           r-genomicranges
+           r-iranges
+           r-rbowtie
+           r-rhtslib
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-shortread))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/QuasR/")
     (synopsis "Quantify and annotate short reads in R")
     (description
@@ -9244,37 +9641,37 @@ quantification of genomic regions of interest.")
 (define-public r-rqc
   (package
     (name "r-rqc")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rqc" version))
        (sha256
         (base32
-         "02hwj2vd003x0zf273ndnwh7kxy6wc3sz14d3kryp2w2aqjj826f"))))
+         "0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071"))))
     (properties `((upstream-name . "Rqc")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biocstyle" ,r-biocstyle)
-       ("r-biostrings" ,r-biostrings)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-knitr" ,r-knitr)
-       ("r-markdown" ,r-markdown)
-       ("r-plyr" ,r-plyr)
-       ("r-rcpp" ,r-rcpp)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-shortread" ,r-shortread)))
+     (list r-biocgenerics
+           r-biocparallel
+           r-biocstyle
+           r-biostrings
+           r-biovizbase
+           r-genomicalignments
+           r-genomicfiles
+           r-ggplot2
+           r-iranges
+           r-knitr
+           r-markdown
+           r-plyr
+           r-rcpp
+           r-reshape2
+           r-rsamtools
+           r-s4vectors
+           r-shiny
+           r-shortread))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/labbcb/Rqc")
     (synopsis "Quality control tool for high-throughput sequencing data")
     (description
@@ -9287,21 +9684,18 @@ graphics.")
 (define-public r-birewire
   (package
     (name "r-birewire")
-    (version "3.24.0")
+    (version "3.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiRewire" version))
        (sha256
         (base32
-         "0p6mr67mkw54490sv4dvkyh8l0xkpjfbqy532vi8l41i40qg3gry"))))
+         "0ki4rcwjgbixzy5q9s30ajx5zhpl18q50znrb60fchvl4hj9h93w"))))
     (properties `((upstream-name . "BiRewire")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-igraph" ,r-igraph)
-       ("r-matrix" ,r-matrix)
-       ("r-slam" ,r-slam)
-       ("r-tsne" ,r-tsne)))
+     (list r-igraph r-matrix r-slam r-tsne))
     (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
     (synopsis "Tools for randomization of bipartite graphs")
     (description
@@ -9326,9 +9720,7 @@ routines to analyse the resulting networks and their natural projections.")
          "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-limma" ,r-limma)
-       ("r-mass" ,r-mass)))
+     (list r-biobase r-limma r-mass))
     (home-page "https://bioconductor.org/packages/birta")
     (synopsis "Bayesian inference of regulation of transcriptional activity")
     (description
@@ -9345,29 +9737,29 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.")
 (define-public r-multidataset
   (package
     (name "r-multidataset")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiDataSet" version))
        (sha256
         (base32
-         "1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj"))))
+         "17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s"))))
     (properties `((upstream-name . "MultiDataSet")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-qqman" ,r-qqman)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-biobase
+           r-biocgenerics
+           r-genomicranges
+           r-ggplot2
+           r-ggrepel
+           r-iranges
+           r-limma
+           r-qqman
+           r-s4vectors
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/MultiDataSet/")
     (synopsis "Implementation of MultiDataSet and ResultSet")
     (description
@@ -9382,20 +9774,19 @@ packages.")
 (define-public r-ropls
   (package
     (name "r-ropls")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32
-         "1j99kdywyljqzdcns5ysh590w4w8iiwzpddpfk5c8d4whax7vk5b"))))
+         "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-multidataset" ,r-multidataset)))
+     (list r-biobase r-multidataset))
     (native-inputs
-     `(("r-knitr" ,r-knitr))) ; for vignettes
+     (list r-knitr)) ; for vignettes
     (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
     (synopsis "Multivariate analysis and feature selection of omics data")
     (description
@@ -9420,23 +9811,19 @@ coefficients).")
 (define-public r-biosigner
   (package
     (name "r-biosigner")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biosigner" version))
        (sha256
         (base32
-         "159fbkymn92li7dinsm56nsacjp8wnhsljv7airgs9m82p8wd5sl"))))
+         "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-e1071" ,r-e1071)
-       ("r-multidataset" ,r-multidataset)
-       ("r-randomforest" ,r-randomforest)
-       ("r-ropls" ,r-ropls)))
+     (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/biosigner/")
     (synopsis "Signature discovery from omics data")
     (description
@@ -9453,31 +9840,31 @@ datasets.")
 (define-public r-annotatr
   (package
     (name "r-annotatr")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotatr" version))
        (sha256
         (base32
-         "1ls1qdfppcxysggi3bghrnspb5a3s40pm2mj4x0whc7c40cf90mg"))))
+         "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationhub" ,r-annotationhub)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-readr" ,r-readr)
-       ("r-regioner" ,r-regioner)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-annotationdbi
+           r-annotationhub
+           r-dplyr
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-readr
+           r-regioner
+           r-reshape2
+           r-rtracklayer
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/annotatr/")
     (synopsis "Annotation of genomic regions to genomic annotations")
     (description
@@ -9494,19 +9881,19 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.6.4")
+    (version "2.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "043m4512q73x6q529hqfgrap0fq5anvny4va085nafia06b805pi"))))
+         "0lpx0dp5570kbrq7v0g573axkhi00qrf38si59vmvnqxhmkvsixn"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
-    (inputs `(("zlib" ,zlib)))
+    (inputs (list zlib))
     (propagated-inputs
-     `(("r-matrix" ,r-matrix)))
+     (list r-matrix))
     (home-page "https://bioconductor.org/packages/Rsubread/")
     (synopsis "Subread sequence alignment and counting for R")
     (description
@@ -9520,23 +9907,23 @@ and to both short and long sequence reads.")
 (define-public r-flowutils
   (package
     (name "r-flowutils")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowUtils" version))
        (sha256
         (base32
-         "1sdwgyvrsz0pp60zdfrcgb7bs8s87j7257p8ck813ydizc324x9w"))))
+         "0rgybkzbn8c3kpbz0ddghp1np0gka0cgiqvkk5jbnhlgf4s07161"))))
     (properties `((upstream-name . "flowUtils")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-corpcor" ,r-corpcor)
-       ("r-flowcore" ,r-flowcore)
-       ("r-graph" ,r-graph)
-       ("r-runit" ,r-runit)
-       ("r-xml" ,r-xml)))
+     (list r-biobase
+           r-corpcor
+           r-flowcore
+           r-graph
+           r-runit
+           r-xml))
     (home-page "https://github.com/jspidlen/flowUtils")
     (synopsis "Utilities for flow cytometry")
     (description
@@ -9546,21 +9933,19 @@ and to both short and long sequence reads.")
 (define-public r-consensusclusterplus
   (package
     (name "r-consensusclusterplus")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ConsensusClusterPlus" version))
        (sha256
         (base32
-         "163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b"))))
+         "13z43qbk9z7mvy8v8k185m6n020i6ahb18pm4q88rs75qlklzdkr"))))
     (properties
      `((upstream-name . "ConsensusClusterPlus")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-all" ,r-all)
-       ("r-biobase" ,r-biobase)
-       ("r-cluster" ,r-cluster)))
+     (list r-all r-biobase r-cluster))
     (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
     (synopsis "Clustering algorithm")
     (description
@@ -9571,25 +9956,25 @@ cluster count and membership by stability evidence in unsupervised analysis.")
 (define-public r-cytolib
   (package
     (name "r-cytolib")
-    (version "2.4.0")
+    (version "2.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cytolib" version))
        (sha256
         (base32
-         "0wl7zqwv0i38dfzqfsz40n3mcbxi38ffn1rbd5pm9s7hq16zr4nv"))))
+         "16m5w6cp28p4fs2p8c8rjcg1d686xl8mpas816i7zxfh8m0bcqc9"))))
     (properties `((upstream-name . "cytolib")))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (propagated-inputs
-     `(("r-bh" ,r-bh)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rcppparallel" ,r-rcppparallel)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-rprotobuflib" ,r-rprotobuflib)))
+     (list r-bh
+           r-rcpp
+           r-rcpparmadillo
+           r-rcppparallel
+           r-rhdf5lib
+           r-rprotobuflib))
     (home-page "https://bioconductor.org/packages/cytolib/")
     (synopsis "C++ infrastructure for working with gated cytometry")
     (description
@@ -9600,28 +9985,28 @@ interact with gated cytometry data.")
 (define-public r-flowcore
   (package
     (name "r-flowcore")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowCore" version))
        (sha256
         (base32
-         "13xpbkxi53rxmhvpdiy6bydmhicmxd2gi96d9c1qx4lkss2f14nc"))))
+         "0zbd2hrdbb6r0np6nd3ab8nlcf9l57vcwnnhbqkbas8y0c2i2mwp"))))
     (properties `((upstream-name . "flowCore")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bh" ,r-bh)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-cytolib" ,r-cytolib)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rprotobuflib" ,r-rprotobuflib)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-bh
+           r-biobase
+           r-biocgenerics
+           r-cytolib
+           r-matrixstats
+           r-rcpp
+           r-rcpparmadillo
+           r-rprotobuflib
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/flowCore")
     (synopsis "Basic structures for flow cytometry data")
     (description
@@ -9632,21 +10017,18 @@ with flow cytometry data.")
 (define-public r-flowmeans
   (package
     (name "r-flowmeans")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowMeans" version))
        (sha256
         (base32
-         "1awskkq48qhv4v9glxgfqi0kgwqd62fbj641k4vvxfcwsf2c7bfg"))))
+         "0iy8hvi0inj1ylhdx6q4mya9k55iazprz6fdrnq1mxb2iyndzsl6"))))
     (properties `((upstream-name . "flowMeans")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-feature" ,r-feature)
-       ("r-flowcore" ,r-flowcore)
-       ("r-rrcov" ,r-rrcov)))
+     (list r-biobase r-feature r-flowcore r-rrcov))
     (home-page "https://bioconductor.org/packages/flowMeans")
     (synopsis "Non-parametric flow cytometry data gating")
     (description
@@ -9658,27 +10040,27 @@ change point detection.")
 (define-public r-ncdfflow
   (package
     (name "r-ncdfflow")
-    (version "2.38.0")
+    (version "2.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ncdfFlow" version))
        (sha256
         (base32
-         "1lm88qnfv6rnnr7wmgbvwyj272imjjjn7h3agxqqzsbmn8vyrnf0"))))
+         "1c6wb2x24ydqp5nxrx6bhj6f13x9djfy9awkc7zn63xkag7mvvar"))))
     (properties `((upstream-name . "ncdfFlow")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bh" ,r-bh)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-flowcore" ,r-flowcore)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list r-bh
+           r-biobase
+           r-biocgenerics
+           r-flowcore
+           r-rcpp
+           r-rcpparmadillo
+           r-rhdf5lib
+           r-zlibbioc))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/ncdfFlow/")
     (synopsis "HDF5 based storage for flow cytometry data")
     (description
@@ -9689,30 +10071,30 @@ manipulation of flow cytometry data.")
 (define-public r-ggcyto
   (package
     (name "r-ggcyto")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggcyto" version))
        (sha256
         (base32
-         "0jd6m84m4znnpix4bcgdby7mnflsn206f5x2vw9n8rxnwzx77wpg"))))
+         "17dnmsa92gc2za36c3klgd7rklqlxrhkzs5ksnrc1am6a4knc0p1"))))
     (properties `((upstream-name . "ggcyto")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-flowcore" ,r-flowcore)
-       ("r-flowworkspace" ,r-flowworkspace)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-hexbin" ,r-hexbin)
-       ("r-ncdfflow" ,r-ncdfflow)
-       ("r-plyr" ,r-plyr)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rlang" ,r-rlang)
-       ("r-scales" ,r-scales)))
+     (list r-data-table
+           r-flowcore
+           r-flowworkspace
+           r-ggplot2
+           r-gridextra
+           r-hexbin
+           r-ncdfflow
+           r-plyr
+           r-rcolorbrewer
+           r-rlang
+           r-scales))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/RGLab/ggcyto/issues")
     (synopsis "Visualize Cytometry data with ggplot")
     (description
@@ -9726,28 +10108,28 @@ statistics to the plot.")
 (define-public r-flowviz
   (package
     (name "r-flowviz")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowViz" version))
        (sha256
         (base32
-         "17x04xwyw2pp5zkhgvrmxkb8cbrv9wql6xhjsfpq0n6yd9dxqc1v"))))
+         "039sh7qn25gp2b34khs8dyrdpxyapsjlprrvxlz8f7dl8gmggl04"))))
     (properties `((upstream-name . "flowViz")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-flowcore" ,r-flowcore)
-       ("r-hexbin" ,r-hexbin)
-       ("r-idpmisc" ,r-idpmisc)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-lattice" ,r-lattice)
-       ("r-latticeextra" ,r-latticeextra)
-       ("r-mass" ,r-mass)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+     (list r-biobase
+           r-flowcore
+           r-hexbin
+           r-idpmisc
+           r-kernsmooth
+           r-lattice
+           r-latticeextra
+           r-mass
+           r-rcolorbrewer))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/flowViz/")
     (synopsis "Visualization for flow cytometry")
     (description
@@ -9757,34 +10139,33 @@ statistics to the plot.")
 (define-public r-flowclust
   (package
     (name "r-flowclust")
-    (version "3.30.0")
+    (version "3.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowClust" version))
        (sha256
         (base32
-         "03xsmprrkxwkaksjlaxwp54mqfb3zlg6dbqhp87w78fwscisv76b"))))
+         "0ch7mkq40qcnxwgzy51vjdlwyzx4bvp03vpdm6dwjc6qy8a6qfzi"))))
     (properties `((upstream-name . "flowClust")))
     (build-system r-build-system)
     (arguments
      `(#:configure-flags
        (list "--configure-args=--enable-bundled-gsl=no")))
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-clue" ,r-clue)
-       ("r-corpcor" ,r-corpcor)
-       ("r-ellipse" ,r-ellipse)
-       ("r-flowcore" ,r-flowcore)
-       ("r-flowviz" ,r-flowviz)
-       ("r-graph" ,r-graph)
-       ("r-mnormt" ,r-mnormt)))
+     (list r-biobase
+           r-biocgenerics
+           r-clue
+           r-corpcor
+           r-ellipse
+           r-flowcore
+           r-flowviz
+           r-graph
+           r-mnormt))
     (inputs
-     `(("gsl" ,gsl)))
+     (list gsl))
     (native-inputs
-     `(("pkg-config" ,pkg-config)
-       ("r-knitr" ,r-knitr)))
+     (list pkg-config r-knitr))
     (home-page "https://bioconductor.org/packages/flowClust")
     (synopsis "Clustering for flow cytometry")
     (description
@@ -9797,14 +10178,14 @@ model with Box-Cox transformation.")
 (define-public r-rprotobuflib
   (package
     (name "r-rprotobuflib")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RProtoBufLib" version))
        (sha256
         (base32
-         "1hyds97ay4mn7nl830yh9v8mlasgsljsx5wsrhz2zsmbbyx6wbnb"))))
+         "04qlhbhdchpr35rdc6jc3y8fy6znnfrdlsb8am04agbrvpjgrx10"))))
     (properties `((upstream-name . "RProtoBufLib")))
     (build-system r-build-system)
     (arguments
@@ -9815,7 +10196,7 @@ model with Box-Cox transformation.")
              (with-directory-excursion "src"
                (invoke "tar" "xf" "protobuf-3.13.0.tar.gz")))))))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/RProtoBufLib/")
     (synopsis "C++ headers and static libraries of Protocol buffers")
     (description
@@ -9826,46 +10207,46 @@ for other R packages to compile and link against.")
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")
-    (version "4.4.0")
+    (version "4.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32
-         "1a9qb2dcvwgb3z0vdbbzn1rzy77d3da72kirs272344hdx9b2cx9"))))
+         "11ni7kgk9s1fz3lvg85s6r7x2fhk4m7cdpilji05ya12jsyr3fig"))))
     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-aws-s3" ,r-aws-s3)
-       ("r-aws-signature" ,r-aws-signature)
-       ("r-bh" ,r-bh)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-cytolib" ,r-cytolib)
-       ("r-data-table" ,r-data-table)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-digest" ,r-digest)
-       ("r-dplyr" ,r-dplyr)
-       ("r-flowcore" ,r-flowcore)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-graph" ,r-graph)
-       ("r-lattice" ,r-lattice)
-       ("r-latticeextra" ,r-latticeextra)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-ncdfflow" ,r-ncdfflow)
-       ("r-rbgl" ,r-rbgl)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rcppparallel" ,r-rcppparallel)
-       ("r-rgraphviz" ,r-rgraphviz)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-rprotobuflib" ,r-rprotobuflib)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-xml" ,r-xml)))
+     (list r-aws-s3
+           r-aws-signature
+           r-bh
+           r-biobase
+           r-biocgenerics
+           r-cytolib
+           r-data-table
+           r-delayedarray
+           r-digest
+           r-dplyr
+           r-flowcore
+           r-ggplot2
+           r-graph
+           r-lattice
+           r-latticeextra
+           r-matrixstats
+           r-ncdfflow
+           r-rbgl
+           r-rcpp
+           r-rcpparmadillo
+           r-rcppparallel
+           r-rgraphviz
+           r-rhdf5lib
+           r-rprotobuflib
+           r-s4vectors
+           r-scales
+           r-xml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/flowWorkspace/")
     (synopsis "Infrastructure for working with cytometry data")
     (description
@@ -9880,31 +10261,31 @@ matches the flowJo analysis.")
 (define-public r-flowstats
   (package
     (name "r-flowstats")
-    (version "4.4.0")
+    (version "4.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowStats" version))
        (sha256
         (base32
-         "1yr5m7qmhmm52c70z3d0zy4zgf0hja7r2ig9yljv5w86bzm962x6"))))
+         "0jjfq66m4lbpkynwxaparkd05znhp3jl9ccj37gyghly294x3rm9"))))
     (properties `((upstream-name . "flowStats")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-cluster" ,r-cluster)
-       ("r-fda" ,r-fda)
-       ("r-flowcore" ,r-flowcore)
-       ("r-flowviz" ,r-flowviz)
-       ("r-flowworkspace" ,r-flowworkspace)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-ks" ,r-ks)
-       ("r-lattice" ,r-lattice)
-       ("r-mass" ,r-mass)
-       ("r-ncdfflow" ,r-ncdfflow)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rrcov" ,r-rrcov)))
+     (list r-biobase
+           r-biocgenerics
+           r-cluster
+           r-fda
+           r-flowcore
+           r-flowviz
+           r-flowworkspace
+           r-kernsmooth
+           r-ks
+           r-lattice
+           r-mass
+           r-ncdfflow
+           r-rcolorbrewer
+           r-rrcov))
     (home-page "http://www.github.com/RGLab/flowStats")
     (synopsis "Statistical methods for the analysis of flow cytometry data")
     (description
@@ -9916,40 +10297,40 @@ package.")
 (define-public r-opencyto
   (package
     (name "r-opencyto")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "openCyto" version))
        (sha256
         (base32
-         "1par1d5pk1rjg15q7i5z5wqma7xg6fycb826a823wk8wr52a885x"))))
+         "11svr1lk383pkm4npwrnf3h37b3drjsmcwcgdbb45x8k2k95z2fm"))))
     (properties `((upstream-name . "openCyto")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-clue" ,r-clue)
-       ("r-data-table" ,r-data-table)
-       ("r-flowclust" ,r-flowclust)
-       ("r-flowcore" ,r-flowcore)
-       ("r-flowstats" ,r-flowstats)
-       ("r-flowviz" ,r-flowviz)
-       ("r-flowworkspace" ,r-flowworkspace)
-       ("r-graph" ,r-graph)
-       ("r-gtools" ,r-gtools)
-       ("r-ks" ,r-ks)
-       ("r-lattice" ,r-lattice)
-       ("r-mass" ,r-mass)
-       ("r-ncdfflow" ,r-ncdfflow)
-       ("r-plyr" ,r-plyr)
-       ("r-r-utils" ,r-r-utils)
-       ("r-rbgl" ,r-rbgl)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rrcov" ,r-rrcov)))
+     (list r-biobase
+           r-biocgenerics
+           r-clue
+           r-data-table
+           r-flowclust
+           r-flowcore
+           r-flowstats
+           r-flowviz
+           r-flowworkspace
+           r-graph
+           r-gtools
+           r-ks
+           r-lattice
+           r-mass
+           r-ncdfflow
+           r-plyr
+           r-r-utils
+           r-rbgl
+           r-rcolorbrewer
+           r-rcpp
+           r-rrcov))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/openCyto")
     (synopsis "Hierarchical gating pipeline for flow cytometry data")
     (description
@@ -9960,49 +10341,48 @@ sequential way to mimic the manual gating strategy.")
 (define-public r-cytoml
   (package
     (name "r-cytoml")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CytoML" version))
        (sha256
         (base32
-         "0ixy7mmnipk8wy61wz6qy7jfbc5zhs6p5iqaii8hdprjnb841ri7"))))
+         "16rgsc2dz5b8lm3ma8nh9wiknrdnvfjcsij7809rmcfs0gn1arcz"))))
     (properties `((upstream-name . "CytoML")))
     (build-system r-build-system)
     (inputs
-     `(("libxml2" ,libxml2)
-       ("zlib" ,zlib)))
+     (list libxml2 zlib))
     (propagated-inputs
-     `(("r-base64enc" ,r-base64enc)
-       ("r-bh" ,r-bh)
-       ("r-biobase" ,r-biobase)
-       ("r-corpcor" ,r-corpcor)
-       ("r-cytolib" ,r-cytolib)
-       ("r-data-table" ,r-data-table)
-       ("r-dplyr" ,r-dplyr)
-       ("r-flowcore" ,r-flowcore)
-       ("r-flowworkspace" ,r-flowworkspace)
-       ("r-ggcyto" ,r-ggcyto)
-       ("r-graph" ,r-graph)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-lattice" ,r-lattice)
-       ("r-opencyto" ,r-opencyto)
-       ("r-plyr" ,r-plyr)
-       ("r-rbgl" ,r-rbgl)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rcppparallel" ,r-rcppparallel)
-       ("r-rgraphviz" ,r-rgraphviz)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-rprotobuflib" ,r-rprotobuflib)
-       ("r-runit" ,r-runit)
-       ("r-tibble" ,r-tibble)
-       ("r-xml" ,r-xml)
-       ("r-xml2" ,r-xml2)
-       ("r-yaml" ,r-yaml)))
+     (list r-base64enc
+           r-bh
+           r-biobase
+           r-corpcor
+           r-cytolib
+           r-data-table
+           r-dplyr
+           r-flowcore
+           r-flowworkspace
+           r-ggcyto
+           r-graph
+           r-jsonlite
+           r-lattice
+           r-opencyto
+           r-plyr
+           r-rbgl
+           r-rcpp
+           r-rcpparmadillo
+           r-rcppparallel
+           r-rgraphviz
+           r-rhdf5lib
+           r-rprotobuflib
+           r-runit
+           r-tibble
+           r-xml
+           r-xml2
+           r-yaml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/RGLab/CytoML")
     (synopsis "GatingML interface for cross platform cytometry data sharing")
     (description
@@ -10013,39 +10393,39 @@ standard to exchange gated cytometry data with other software platforms.")
 (define-public r-flowsom
   (package
     (name "r-flowsom")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "FlowSOM" version))
        (sha256
         (base32
-         "18h7p7g3w9imyd1c93jllgp4kd74z96cs85wcqfhmd26nx18hl82"))))
+         "062xrv8li2z849qa8mv5dhafqli6ziz099ikjfvi7v2fr7174p8f"))))
     (properties `((upstream-name . "FlowSOM")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-colorramps" ,r-colorramps)
-       ("r-consensusclusterplus" ,r-consensusclusterplus)
-       ("r-cytoml" ,r-cytoml)
-       ("r-dplyr" ,r-dplyr)
-       ("r-flowcore" ,r-flowcore)
-       ("r-flowworkspace" ,r-flowworkspace)
-       ("r-ggforce" ,r-ggforce)
-       ("r-ggnewscale" ,r-ggnewscale)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggpointdensity" ,r-ggpointdensity)
-       ("r-ggpubr" ,r-ggpubr)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-igraph" ,r-igraph)
-       ("r-magrittr" ,r-magrittr)
-       ("r-pheatmap" ,r-pheatmap)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rlang" ,r-rlang)
-       ("r-rtsne" ,r-rtsne)
-       ("r-scattermore" ,r-scattermore)
-       ("r-tidyr" ,r-tidyr)
-       ("r-xml" ,r-xml)))
+     (list r-biocgenerics
+           r-colorramps
+           r-consensusclusterplus
+           r-cytoml
+           r-dplyr
+           r-flowcore
+           r-flowworkspace
+           r-ggforce
+           r-ggnewscale
+           r-ggplot2
+           r-ggpointdensity
+           r-ggpubr
+           r-ggrepel
+           r-igraph
+           r-magrittr
+           r-pheatmap
+           r-rcolorbrewer
+           r-rlang
+           r-rtsne
+           r-scattermore
+           r-tidyr
+           r-xml))
     (home-page "https://bioconductor.org/packages/FlowSOM/")
     (synopsis "Visualize and interpret cytometry data")
     (description
@@ -10056,34 +10436,34 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.16.3")
+    (version "6.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "1x6dbw4q6p9vngm256fr96r9fjxk5nik5ivkhbl5a9zqyq8wagpa"))))
+         "1wpskrnl2bry9m4k2djhjddcd8gpwf51gp5c3si1y7qxja78ql9f"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-corpcor" ,r-corpcor)
-       ("r-dplyr" ,r-dplyr)
-       ("r-ellipse" ,r-ellipse)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-igraph" ,r-igraph)
-       ("r-lattice" ,r-lattice)
-       ("r-mass" ,r-mass)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rarpack" ,r-rarpack)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-reshape2" ,r-reshape2)
-       ("r-tidyr" ,r-tidyr)))
+     (list r-biocparallel
+           r-corpcor
+           r-dplyr
+           r-ellipse
+           r-ggrepel
+           r-ggplot2
+           r-gridextra
+           r-igraph
+           r-lattice
+           r-mass
+           r-matrixstats
+           r-rarpack
+           r-rcolorbrewer
+           r-reshape2
+           r-tidyr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "http://www.mixOmics.org")
     (synopsis "Multivariate methods for exploration of biological datasets")
     (description
@@ -10102,36 +10482,36 @@ delete entire rows with missing data.")
 (define-public r-depecher
   (package                              ;Source/Weave error
     (name "r-depecher")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DepecheR" version))
        (sha256
         (base32
-         "04vxc43p3kpsx0vksk2nwmy9p56h35z2mc8j9p2wm29zaz1y8j3p"))))
+         "1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9"))))
     (properties `((upstream-name . "DepecheR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-beanplot" ,r-beanplot)
-       ("r-dosnow" ,r-dosnow)
-       ("r-dplyr" ,r-dplyr)
-       ("r-fnn" ,r-fnn)
-       ("r-foreach" ,r-foreach)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gmodels" ,r-gmodels)
-       ("r-gplots" ,r-gplots)
-       ("r-mass" ,r-mass)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-mixomics" ,r-mixomics)
-       ("r-moments" ,r-moments)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcppeigen" ,r-rcppeigen)
-       ("r-reshape2" ,r-reshape2)
-       ("r-robustbase" ,r-robustbase)
-       ("r-viridis" ,r-viridis)))
+     (list r-beanplot
+           r-dosnow
+           r-dplyr
+           r-fnn
+           r-foreach
+           r-ggplot2
+           r-gmodels
+           r-gplots
+           r-mass
+           r-matrixstats
+           r-mixomics
+           r-moments
+           r-rcpp
+           r-rcppeigen
+           r-reshape2
+           r-robustbase
+           r-viridis))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/DepecheR/")
     (synopsis "Identify traits of clusters in high-dimensional entities")
     (description
@@ -10148,31 +10528,31 @@ data, to only emphasize the data that actually matters.")
 (define-public r-rcistarget
   (package
     (name "r-rcistarget")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RcisTarget" version))
        (sha256
         (base32
-         "1yh0l11vnslgr6zsbpgc8mc4aa32zy34f5yrz98hkcdl53iw5y7f"))))
+         "1qarr7xd71kz1haccj65x7sc7pc4v6xpqcfa3rkyp2bk240gigi7"))))
     (properties `((upstream-name . "RcisTarget")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-arrow" ,r-arrow)
-       ("r-aucell" ,r-aucell)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-data-table" ,r-data-table)
-       ("r-dplyr" ,r-dplyr)
-       ("r-feather" ,r-feather)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gseabase" ,r-gseabase)
-       ("r-r-utils" ,r-r-utils)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-tibble" ,r-tibble)))
+     (list r-arrow
+           r-aucell
+           r-biocgenerics
+           r-data-table
+           r-dplyr
+           r-feather
+           r-genomeinfodb
+           r-genomicranges
+           r-gseabase
+           r-r-utils
+           r-summarizedexperiment
+           r-tibble))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://aertslab.org/#scenic")
     (synopsis "Identify transcription factor binding motifs enriched on a gene list")
     (description
@@ -10190,23 +10570,19 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-chicago
   (package
     (name "r-chicago")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Chicago" version))
        (sha256
         (base32
-         "0dkwy6pfvzd7g4qmhjl24ypn92l78w1zy0ajhcxgg39f7zsq883x"))))
+         "0nz9v37p7zl8yw3ykdbsb3izcwgx349wvrhwfyyn9h3jxjfafngn"))))
     (properties `((upstream-name . "Chicago")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-delaporte" ,r-delaporte)
-       ("r-hmisc" ,r-hmisc)
-       ("r-mass" ,r-mass)
-       ("r-matrixstats" ,r-matrixstats)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/Chicago")
     (synopsis "Capture Hi-C analysis of genomic organization")
     (description
@@ -10216,40 +10592,40 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "1y34cm52bv1v2hr7sz8zjzxwd4wng7v75avz5wx45l0ld54z9l10"))))
+         "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-assertthat" ,r-assertthat)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-data-table" ,r-data-table)
-       ("r-dplyr" ,r-dplyr)
-       ("r-fnn" ,r-fnn)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-glasso" ,r-glasso)
-       ("r-gviz" ,r-gviz)
-       ("r-igraph" ,r-igraph)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-monocle" ,r-monocle)
-       ("r-plyr" ,r-plyr)
-       ("r-reshape2" ,r-reshape2)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-stringi" ,r-stringi)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)
-       ("r-vgam" ,r-vgam)))
+     (list r-assertthat
+           r-biobase
+           r-biocgenerics
+           r-data-table
+           r-dplyr
+           r-fnn
+           r-genomicranges
+           r-ggplot2
+           r-glasso
+           r-gviz
+           r-igraph
+           r-iranges
+           r-matrix
+           r-monocle
+           r-plyr
+           r-reshape2
+           r-s4vectors
+           r-stringi
+           r-stringr
+           r-tibble
+           r-tidyr
+           r-vgam))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/cicero/")
     (synopsis "Predict cis-co-accessibility from single-cell data")
     (description
@@ -10276,50 +10652,50 @@ accessibility data.")
           (base32
            "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
       (propagated-inputs
-       `(("r-monocle3" ,r-monocle3)
-         ,@(alist-delete "r-monocle"
-                         (package-propagated-inputs r-cicero)))))))
+       (modify-inputs (package-propagated-inputs r-cicero)
+         (delete "r-monocle")
+         (prepend r-monocle3))))))
 
 (define-public r-circrnaprofiler
   (package
     (name "r-circrnaprofiler")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "circRNAprofiler" version))
        (sha256
         (base32
-         "1hif40vfg2lkbyf6abbkxbdm3b1biw6gxnh6ca2sydvi3y5l2ys2"))))
+         "0l83r9idhrha1m21vpnw917m5dlldji49zvx4d25m5g3ia1pkhpf"))))
     (properties
      `((upstream-name . "circRNAprofiler")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationhub" ,r-annotationhub)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-deseq2" ,r-deseq2)
-       ("r-dplyr" ,r-dplyr)
-       ("r-edger" ,r-edger)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gwascat" ,r-gwascat)
-       ("r-iranges" ,r-iranges)
-       ("r-magrittr" ,r-magrittr)
-       ("r-r-utils" ,r-r-utils)
-       ("r-readr" ,r-readr)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rlang" ,r-rlang)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-seqinr" ,r-seqinr)
-       ("r-stringi" ,r-stringi)
-       ("r-stringr" ,r-stringr)
-       ("r-universalmotif" ,r-universalmotif)))
+     (list r-annotationhub
+           r-biostrings
+           r-bsgenome
+           r-bsgenome-hsapiens-ucsc-hg19
+           r-deseq2
+           r-dplyr
+           r-edger
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-gwascat
+           r-iranges
+           r-magrittr
+           r-r-utils
+           r-readr
+           r-reshape2
+           r-rlang
+           r-rtracklayer
+           r-s4vectors
+           r-seqinr
+           r-stringi
+           r-stringr
+           r-universalmotif))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page
      "https://github.com/Aufiero/circRNAprofiler")
     (synopsis
@@ -10349,21 +10725,21 @@ analysis, evolutionary conservation, biogenesis to functional analysis.")
          "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-aucell" ,r-aucell)
-       ("r-data-table" ,r-data-table)
-       ("r-dplyr" ,r-dplyr)
-       ("r-dosnow" ,r-dosnow)
-       ("r-dt" ,r-dt)
-       ("r-feather" ,r-feather)
-       ("r-fitdistrplus" ,r-fitdistrplus)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-lda" ,r-lda)
-       ("r-matrix" ,r-matrix)
-       ("r-plyr" ,r-plyr)
-       ("r-rcistarget" ,r-rcistarget)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-aucell
+           r-data-table
+           r-dplyr
+           r-dosnow
+           r-dt
+           r-feather
+           r-fitdistrplus
+           r-genomicranges
+           r-ggplot2
+           r-lda
+           r-matrix
+           r-plyr
+           r-rcistarget
+           r-rtracklayer
+           r-s4vectors))
     (home-page "https://github.com/aertslab/cisTopic")
     (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
     (description
@@ -10396,43 +10772,42 @@ cisTopics and explore the nature and regulatory proteins driving them.")
            "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
       (properties `((upstream-name . "cisTopic")))
       (propagated-inputs
-       `(("r-aucell" ,r-aucell)
-         ("r-data-table" ,r-data-table)
-         ("r-dosnow" ,r-dosnow)
-         ("r-dplyr" ,r-dplyr)
-         ("r-dt" ,r-dt)
-         ("r-feather" ,r-feather)
-         ("r-fitdistrplus" ,r-fitdistrplus)
-         ("r-genomicranges" ,r-genomicranges)
-         ("r-ggplot2" ,r-ggplot2)
-         ("r-lda" ,r-lda)
-         ("r-matrix" ,r-matrix)
-         ("r-plyr" ,r-plyr)
-         ("r-rcistarget" ,r-rcistarget)
-         ("r-rtracklayer" ,r-rtracklayer)
-         ("r-s4vectors" ,r-s4vectors)
-         ("r-text2vec" ,r-text2vec)))
+       (list r-aucell
+             r-data-table
+             r-dosnow
+             r-dplyr
+             r-dt
+             r-feather
+             r-fitdistrplus
+             r-genomicranges
+             r-ggplot2
+             r-lda
+             r-matrix
+             r-plyr
+             r-rcistarget
+             r-rtracklayer
+             r-s4vectors
+             r-text2vec))
       (native-inputs
-       `(("r-knitr" ,r-knitr))))))
+       (list r-knitr)))))
 
 (define-public r-genie3
   (package
     (name "r-genie3")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GENIE3" version))
        (sha256
         (base32
-         "1v54dzcz654wfm3npbp8gb55v49im0fm547cz3hvsidq4zhi3l1b"))))
+         "0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw"))))
     (properties `((upstream-name . "GENIE3")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-dplyr" ,r-dplyr)
-       ("r-reshape2" ,r-reshape2)))
+     (list r-dplyr r-reshape2))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/GENIE3")
     (synopsis "Gene network inference with ensemble of trees")
     (description
@@ -10443,18 +10818,18 @@ regulatory networks from expression data.")
 (define-public r-roc
   (package
     (name "r-roc")
-    (version "1.68.1")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROC" version))
        (sha256
         (base32
-         "1rmsrvn6hrg9ay7xfb05mfkxknnig78p3kbk9ghsd11lhx2fjm3s"))))
+         "1mgxpv5p6gnv04wzkcryrg5as5xrxvlqlkkcbv0k1bx9y6ykijy9"))))
     (properties `((upstream-name . "ROC")))
     (build-system r-build-system)
-    (propagated-inputs
-     `(("r-knitr" ,r-knitr)))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://www.bioconductor.org/packages/ROC/")
     (synopsis "Utilities for ROC curves")
     (description
@@ -10479,7 +10854,7 @@ Characteristic} (ROC) curves, with a focus on micro arrays.")
      `((upstream-name
         . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-minfi" ,r-minfi)))
+    (propagated-inputs (list r-minfi))
     (home-page
      "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
     (synopsis "Annotation for Illumina's 450k methylation arrays")
@@ -10491,26 +10866,27 @@ data.")
 (define-public r-watermelon
   (package
     (name "r-watermelon")
-    (version "1.36.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wateRmelon" version))
        (sha256
         (base32
-         "1qar8z0nf33bqr488swig0bfq8lnvcdjcxvw3q3b0hkkvybn27zw"))))
+         "1kzkg3cnm5pcs6blpw1qn7na6z3kar93v67680wsxa6qxxdiggk3"))))
     (properties `((upstream-name . "wateRmelon")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
-        ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
-       ("r-illuminaio" ,r-illuminaio)
-       ("r-limma" ,r-limma)
-       ("r-lumi" ,r-lumi)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-methylumi" ,r-methylumi)
-       ("r-roc" ,r-roc)))
+     (list r-biobase
+           r-illuminahumanmethylation450kanno-ilmn12-hg19
+           r-illuminaio
+           r-limma
+           r-lumi
+           r-matrixstats
+           r-methylumi
+           r-roc))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/wateRmelon/")
     (synopsis "Illumina 450 methylation array normalization and metrics")
     (description
@@ -10528,14 +10904,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
 (define-public r-gdsfmt
   (package
     (name "r-gdsfmt")
-    (version "1.28.1")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gdsfmt" version))
        (sha256
         (base32
-         "1w3z718q3bhh8bp71va9pbcd62pwbvgjw33ffg960jya40xssvc7"))
+         "147i33sb65n3cl3ibmjzgfm7i4ljy640k18mzknvc18v1906j9vp"))
        (modules '((guix build utils)))
        ;; Remove bundled sources of zlib, lz4, and xz.  Don't attempt to build
        ;; them and link with system libraries instead.
@@ -10561,11 +10937,9 @@ metrics, with methods for objects produced by the @code{methylumi} and
     (properties `((upstream-name . "gdsfmt")))
     (build-system r-build-system)
     (inputs
-     `(("lz4" ,lz4)
-       ("xz" ,xz)
-       ("zlib" ,zlib)))
+     (list lz4 xz zlib))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "http://corearray.sourceforge.net/")
     (synopsis
      "R Interface to CoreArray Genomic Data Structure (GDS) Files")
@@ -10586,24 +10960,27 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-bigmelon
   (package
     (name "r-bigmelon")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigmelon" version))
        (sha256
         (base32
-         "061f0hc4m4nvdr6298pg3inpx1z2bpsm9nlxqs3v7n58q15xyzri"))))
+         "0ksbmybi8wsg515b4k9ij1xqqk9i90pyap2wq5w3c49qgc0pqali"))))
     (properties `((upstream-name . "bigmelon")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-gdsfmt" ,r-gdsfmt)
-       ("r-geoquery" ,r-geoquery)
-       ("r-methylumi" ,r-methylumi)
-       ("r-minfi" ,r-minfi)
-       ("r-watermelon" ,r-watermelon)))
+     (list r-biobase
+           r-biocgenerics
+           r-gdsfmt
+           r-geoquery
+           r-illuminaio
+           r-methylumi
+           r-minfi
+           r-watermelon))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/bigmelon/")
     (synopsis "Illumina methylation array analysis for large experiments")
     (description
@@ -10614,20 +10991,18 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-seqbias
   (package
     (name "r-seqbias")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqbias" version))
        (sha256
         (base32
-         "06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k"))))
+         "1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr"))))
     (properties `((upstream-name . "seqbias")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-rhtslib" ,r-rhtslib)))
+     (list r-biostrings r-genomicranges r-rhtslib))
     (home-page "https://bioconductor.org/packages/seqbias/")
     (synopsis "Estimation of per-position bias in high-throughput sequencing data")
     (description
@@ -10653,13 +11028,13 @@ genome sequence.")
     ;; doesn't make sense to build substitutes.
     (arguments `(#:substitutable? #f))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-iranges" ,r-iranges)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-biostrings" ,r-biostrings)))
+     (list r-biocgenerics
+           r-s4vectors
+           r-iranges
+           r-genomeinfodb
+           r-genomicranges
+           r-bsgenome
+           r-biostrings))
     (home-page
      "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
     (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
@@ -10678,20 +11053,18 @@ injected in that sequence).")
 (define-public r-reqon
   (package
     (name "r-reqon")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReQON" version))
        (sha256
         (base32
-         "1z13avbxwvvhh03arjfnaipznynifsi8k2hzw4kappz24f7lwmza"))))
+         "14v79vg3pmpkbzgn8xqd020jdwcs8g57d46bzl23yi3w1rsfbrb1"))))
     (properties `((upstream-name . "ReQON")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-rjava" ,r-rjava)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-seqbias" ,r-seqbias)))
+     (list r-rjava r-rsamtools r-seqbias))
     (home-page "https://bioconductor.org/packages/ReQON/")
     (synopsis "Recalibrating quality of nucleotides")
     (description
@@ -10703,33 +11076,33 @@ format.")
 (define-public r-wavcluster
   (package
     (name "r-wavcluster")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wavClusteR" version))
        (sha256
         (base32
-         "1sydzrqydfv1ik2h08xkxlx6xrv866bf0if6v5wch9l3krh0sych"))))
+         "1a1zhckrgq5yl51acj5piyh2hq70q6hhpym4cawzdssxhcbq70bk"))))
     (properties `((upstream-name . "wavClusteR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-foreach" ,r-foreach)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-hmisc" ,r-hmisc)
-       ("r-iranges" ,r-iranges)
-       ("r-mclust" ,r-mclust)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-seqinr" ,r-seqinr)
-       ("r-stringr" ,r-stringr)))
+     (list r-biocgenerics
+           r-biostrings
+           r-foreach
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-hmisc
+           r-iranges
+           r-mclust
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-seqinr
+           r-stringr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/wavClusteR/")
     (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
     (description
@@ -10750,35 +11123,35 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
 (define-public r-timeseriesexperiment
   (package
     (name "r-timeseriesexperiment")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TimeSeriesExperiment" version))
        (sha256
         (base32
-         "1095a2ynxcf9xiac5cjzslcbmjnjpbby0vy7d84qagdiq1w6mrhn"))))
+         "0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d"))))
     (properties
      `((upstream-name . "TimeSeriesExperiment")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-deseq2" ,r-deseq2)
-       ("r-dplyr" ,r-dplyr)
-       ("r-dynamictreecut" ,r-dynamictreecut)
-       ("r-edger" ,r-edger)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-hmisc" ,r-hmisc)
-       ("r-limma" ,r-limma)
-       ("r-magrittr" ,r-magrittr)
-       ("r-proxy" ,r-proxy)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)
-       ("r-vegan" ,r-vegan)
-       ("r-viridis" ,r-viridis)))
+     (list r-deseq2
+           r-dplyr
+           r-dynamictreecut
+           r-edger
+           r-ggplot2
+           r-hmisc
+           r-limma
+           r-magrittr
+           r-proxy
+           r-s4vectors
+           r-summarizedexperiment
+           r-tibble
+           r-tidyr
+           r-vegan
+           r-viridis))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
     (synopsis "Analysis for short time-series data")
     (description
@@ -10791,42 +11164,42 @@ provides methods for retrieving enriched pathways.")
 (define-public r-variantfiltering
   (package
     (name "r-variantfiltering")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantFiltering" version))
        (sha256
         (base32
-         "0abhrk53csd9jz9sv4q1qr74jax9mbj2icbz1iilf1123nvnjypd"))))
+         "15js8xzi9rsgkjkqcshzk3r3g85kdnxn5v2hi6l5s4yxj9lnq12p"))))
     (properties
      `((upstream-name . "VariantFiltering")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-dt" ,r-dt)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-genomicscores" ,r-genomicscores)
-       ("r-graph" ,r-graph)
-       ("r-gviz" ,r-gviz)
-       ("r-iranges" ,r-iranges)
-       ("r-rbgl" ,r-rbgl)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-shinyjs" ,r-shinyjs)
-       ("r-shinythemes" ,r-shinythemes)
-       ("r-shinytree" ,r-shinytree)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)
-       ("r-xvector" ,r-xvector)))
+     (list r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-bsgenome
+           r-dt
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-genomicscores
+           r-graph
+           r-gviz
+           r-iranges
+           r-rbgl
+           r-rsamtools
+           r-s4vectors
+           r-shiny
+           r-shinyjs
+           r-shinythemes
+           r-shinytree
+           r-summarizedexperiment
+           r-variantannotation
+           r-xvector))
     (home-page "https://github.com/rcastelo/VariantFiltering")
     (synopsis "Filtering of coding and non-coding genetic variants")
     (description
@@ -10849,7 +11222,7 @@ populations, splice site strength, conservation, etc.")
     (properties `((upstream-name . "GenomeGraphs")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biomart" ,r-biomart)))
+     (list r-biomart))
     (home-page "https://bioconductor.org/packages/GenomeGraphs/")
     (synopsis "Plotting genomic information from Ensembl")
     (description
@@ -10877,16 +11250,16 @@ same genome coordinate system.")
     (properties `((upstream-name . "waveTiling")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-biobase" ,r-biobase)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomegraphs" ,r-genomegraphs)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-oligo" ,r-oligo)
-       ("r-oligoclasses" ,r-oligoclasses)
-       ("r-preprocesscore" ,r-preprocesscore)
-       ("r-waveslim" ,r-waveslim)))
+     (list r-affy
+           r-biobase
+           r-biostrings
+           r-genomegraphs
+           r-genomicranges
+           r-iranges
+           r-oligo
+           r-oligoclasses
+           r-preprocesscore
+           r-waveslim))
     (home-page "https://r-forge.r-project.org/projects/wavetiling/")
     (synopsis "Wavelet-based models for tiling array transcriptome analysis")
     (description
@@ -10897,36 +11270,37 @@ arrays based on fast wavelet-based functional models.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "1pqy2g9pg8pswmkrs2fzlkwwliw2r7f33h05bci5bz41b8ribpzj"))))
+         "0f5y61dpzwmr8v7npim18zvxa8n49rbzclb9j72haba0px6ibhvw"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-colorramps" ,r-colorramps)
-       ("r-doparallel" ,r-doparallel)
-       ("r-foreach" ,r-foreach)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gplots" ,r-gplots)
-       ("r-iterators" ,r-iterators)
-       ("r-limma" ,r-limma)
-       ("r-lme4" ,r-lme4)
-       ("r-lmertest" ,r-lmertest)
-       ("r-mass" ,r-mass)
-       ("r-pbkrtest" ,r-pbkrtest)
-       ("r-progress" ,r-progress)
-       ("r-reshape2" ,r-reshape2)
-       ("r-scales" ,r-scales)))
+     (list r-biobase
+           r-biocparallel
+           r-doparallel
+           r-foreach
+           r-ggplot2
+           r-gplots
+           r-iterators
+           r-limma
+           r-lme4
+           r-lmertest
+           r-mass
+           r-matrix
+           r-pbkrtest
+           r-progress
+           r-reshape2
+           r-rlang
+           r-scales))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/variancePartition/")
     (synopsis "Analyze variation in gene expression experiments")
     (description
@@ -10941,22 +11315,18 @@ measures.")
 (define-public r-htqpcr
   (package
     (name "r-htqpcr")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HTqPCR" version))
        (sha256
         (base32
-         "1y3ik5a9w66jby6682jfm8mn2883s8yfv4xw8a8v1f6q2d1j938l"))))
+         "1d7qj5yv6kzqmdrnp5pd8qv1yr4bg8cs39p8ib0i0k8b4wr97kq3"))))
     (properties `((upstream-name . "HTqPCR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-biobase" ,r-biobase)
-       ("r-gplots" ,r-gplots)
-       ("r-limma" ,r-limma)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+     (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
     (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
                               "groups/bertone/software/HTqPCR.pdf"))
     (synopsis "Automated analysis of high-throughput qPCR data")
@@ -10975,20 +11345,19 @@ features (e.g.  genes, microRNAs).")
 (define-public r-unifiedwmwqpcr
   (package
     (name "r-unifiedwmwqpcr")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "unifiedWMWqPCR" version))
        (sha256
         (base32
-         "1clcz610sl3s0mjf84j21xgrmjhkxcc4h292ljwq5yzbkk68g896"))))
+         "0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk"))))
     (properties
      `((upstream-name . "unifiedWMWqPCR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-htqpcr" ,r-htqpcr)))
+     (list r-biocgenerics r-htqpcr))
     (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
     (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
     (description
@@ -11000,14 +11369,14 @@ data.")
 (define-public r-universalmotif
   (package
     (name "r-universalmotif")
-    (version "1.10.2")
+    (version "1.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "universalmotif" version))
        (sha256
         (base32
-         "0hv2v2zgif5ihr5hxmdz32rln43jc1j0rslp44kd3rijjl45zysn"))))
+         "1p9zdrsxqn4ayvbj05xgpzpbzkzrh7k0d62x10069687vfl6dlxg"))))
     (properties
      `((upstream-name . "universalmotif")))
     (build-system r-build-system)
@@ -11019,18 +11388,18 @@ data.")
              (substitute* "src/Makevars"
                (("/usr/bin/strip") (which "strip"))))))))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-mass" ,r-mass)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcppthread" ,r-rcppthread)
-       ("r-rlang" ,r-rlang)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-yaml" ,r-yaml)))
+     (list r-biocgenerics
+           r-biostrings
+           r-ggplot2
+           r-iranges
+           r-mass
+           r-rcpp
+           r-rcppthread
+           r-rlang
+           r-s4vectors
+           r-yaml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page
      "https://bioconductor.org/packages/universalmotif/")
     (synopsis
@@ -11050,27 +11419,30 @@ motifs, and others.")
 (define-public r-activedriverwgs
   (package
     (name "r-activedriverwgs")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActiveDriverWGS" version))
        (sha256
         (base32
-         "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
+         "13b5yazgv9kckcp6gck183mh1m0q8lc5ixagmcy9s8kv2wz7wq45"))))
     (properties
      `((upstream-name . "ActiveDriverWGS")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biostrings
+           r-bsgenome
+           r-bsgenome-hsapiens-ucsc-hg19
+           r-bsgenome-hsapiens-ucsc-hg38
+           r-bsgenome-mmusculus-ucsc-mm9
+           r-bsgenome-mmusculus-ucsc-mm10
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
     (synopsis "Driver discovery tool for cancer whole genomes")
     (description
@@ -11085,22 +11457,21 @@ using whole genome sequencing data.")
 (define-public r-activepathways
   (package
     (name "r-activepathways")
-    (version "1.0.2")
+    (version "1.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActivePathways" version))
        (sha256
         (base32
-         "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
+         "1prhwx0nnwy2q62l2r0z31mhk4mq6xdr6mjihdlwpwgwq4rfi60y"))))
     (properties
      `((upstream-name . "ActivePathways")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-ggplot2" ,r-ggplot2)))
+     (list r-data-table r-ggplot2))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
     (synopsis "Multivariate pathway enrichment analysis")
     (description
@@ -11114,18 +11485,18 @@ cellular organization in health and disease.")
 (define-public r-bgmix
   (package
     (name "r-bgmix")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BGmix" version))
        (sha256
         (base32
-         "1gp40ddspblpszzm4k4r7ysgx883iwdfqc5ds23p2q1ml9idwgvv"))))
+         "0x1sx319yfxgkscr9r62msq00ddvmzryzn42wy4dh5pvjmgifkkn"))))
     (properties `((upstream-name . "BGmix")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-kernsmooth" ,r-kernsmooth)))
+     (list r-kernsmooth))
     (home-page "https://bioconductor.org/packages/BGmix/")
     (synopsis "Bayesian models for differential gene expression")
     (description
@@ -11136,21 +11507,18 @@ gene expression.")
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "18n6j2ihv85rhai5sf5k3mwf9nkc2nl2sinx3rrs6sbl529g4mw4"))))
+         "0z3isnpyf9s11807dprxmd105lb0k4l7r1sygad30ncjvpldifzm"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-biobase" ,r-biobase)
-       ("r-gcrma" ,r-gcrma)
-       ("r-rcpp" ,r-rcpp)))
+     (list r-affy r-biobase r-gcrma r-rcpp))
     (home-page "https://bioconductor.org/packages/bgx/")
     (synopsis "Bayesian gene expression")
     (description
@@ -11161,14 +11529,14 @@ Affymetrix GeneChips.")
 (define-public r-bhc
   (package
     (name "r-bhc")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BHC" version))
        (sha256
         (base32
-         "0aaawm7h3ppyyhd7hi14rpynagnxx4730f5vxizj5bpzwbclp6h9"))))
+         "09nw4ljc9sn7iw09ha0m614hmdjj193xhhav5x5p07l501kks6h2"))))
     (properties `((upstream-name . "BHC")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BHC/")
@@ -11187,20 +11555,18 @@ algorithm which is more efficient for larger data sets.")
 (define-public r-bicare
   (package
     (name "r-bicare")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BicARE" version))
        (sha256
         (base32
-         "0j3gs4xcdgaca2c62jf2h86skbbxm1c9g2khs5bsa8fmkskr6vl9"))))
+         "1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6"))))
     (properties `((upstream-name . "BicARE")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-gseabase" ,r-gseabase)
-       ("r-multtest" ,r-multtest)))
+     (list r-biobase r-gseabase r-multtest))
     (home-page "http://bioinfo.curie.fr")
     (synopsis "Biclustering analysis and results exploration")
     (description
@@ -11211,21 +11577,20 @@ results.")
 (define-public r-bifet
   (package
     (name "r-bifet")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiFET" version))
        (sha256
         (base32
-         "1fwy7ws0bn67557s0kcw8pbln2jg834n6kfbs8297ps07nxr0lpj"))))
+         "0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk"))))
     (properties `((upstream-name . "BiFET")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-genomicranges" ,r-genomicranges)
-       ("r-poibin" ,r-poibin)))
+     (list r-genomicranges r-poibin))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiFET")
     (synopsis "Bias-free footprint enrichment test")
     (description
@@ -11241,23 +11606,22 @@ the read count and GC content bias.")
 (define-public r-rsbml
   (package
     (name "r-rsbml")
-    (version "2.50.0")
+    (version "2.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rsbml" version))
        (sha256
         (base32
-         "017xwra6ms7kx6sg3ksw1vr9zn23imc2qjgpmjikx7mgbak125xh"))))
+         "0mdyr637sgasc156cv8i2s2mpl1hdvilfwwkhvw7l95pl90gnsh2"))))
     (properties `((upstream-name . "rsbml")))
     (build-system r-build-system)
     (inputs
-     `(("libsbml" ,libsbml)))
+     (list libsbml))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-graph" ,r-graph)))
+     (list r-biocgenerics r-graph))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     (list pkg-config))
     (home-page "http://www.sbml.org")
     (synopsis "R support for SBML")
     (description
@@ -11268,18 +11632,18 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
 (define-public r-hypergraph
   (package
     (name "r-hypergraph")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hypergraph" version))
        (sha256
         (base32
-         "01knpd964m2g9vwd7c72qnc8g2p2pzhvk7lin4mhvcmb3pvsdlh7"))))
+         "0xnyl9qh5p32ifvzkcl5g4a38zbnwykqzrp8gwz076a0ksiqqdxf"))))
     (properties `((upstream-name . "hypergraph")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-graph" ,r-graph)))
+     (list r-graph))
     (home-page "https://bioconductor.org/packages/hypergraph")
     (synopsis "Hypergraph data structures")
     (description
@@ -11290,21 +11654,19 @@ manipulating hypergraphs.")
 (define-public r-hyperdraw
   (package
     (name "r-hyperdraw")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hyperdraw" version))
        (sha256
         (base32
-         "1qkxixkgvvfha0ii8rwwcbrbjmbbxsy8afv5ymcq01k3hbykx44r"))))
+         "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj"))))
     (properties `((upstream-name . "hyperdraw")))
     (build-system r-build-system)
-    (inputs `(("graphviz" ,graphviz)))
+    (inputs (list graphviz))
     (propagated-inputs
-     `(("r-graph" ,r-graph)
-       ("r-hypergraph" ,r-hypergraph)
-       ("r-rgraphviz" ,r-rgraphviz)))
+     (list r-graph r-hypergraph r-rgraphviz))
     (home-page "https://bioconductor.org/packages/hyperdraw")
     (synopsis "Visualizing hypergraphs")
     (description
@@ -11314,23 +11676,23 @@ manipulating hypergraphs.")
 (define-public r-biggr
   (package
     (name "r-biggr")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiGGR" version))
        (sha256
         (base32
-         "1y9659pxm65w51zvrz36girb3qvfc64zijjkxmg6xn4pbc8vv1wf"))))
+         "1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr"))))
     (properties `((upstream-name . "BiGGR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-hyperdraw" ,r-hyperdraw)
-       ("r-hypergraph" ,r-hypergraph)
-       ("r-lim" ,r-lim)
-       ("r-limsolve" ,r-limsolve)
-       ("r-rsbml" ,r-rsbml)
-       ("r-stringr" ,r-stringr)))
+     (list r-hyperdraw
+           r-hypergraph
+           r-lim
+           r-limsolve
+           r-rsbml
+           r-stringr))
     (home-page "https://bioconductor.org/packages/BiGGR/")
     (synopsis "Constraint based modeling using metabolic reconstruction databases")
     (description
@@ -11356,9 +11718,9 @@ networks and estimated fluxes can be visualized with hypergraphs.")
      `((upstream-name . "bigmemoryExtras")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bigmemory" ,r-bigmemory)))
+     (list r-bigmemory))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/phaverty/bigmemoryExtras")
     (synopsis "Extension of the bigmemory package")
     (description
@@ -11378,37 +11740,37 @@ a file-backed matrix with factor properties.")
 (define-public r-bigpint
   (package
     (name "r-bigpint")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigPint" version))
        (sha256
         (base32
-         "0yrg9x1a92zmz7j5hk77cph1jg82mkpr7k7qi9fdr6z5nqq6fgz6"))))
+         "0b0l0v9p7a5da3x18d0pqn41ilgxfyzapjaawgsshcfm5mjq5d7q"))))
     (properties `((upstream-name . "bigPint")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-delayedarray" ,r-delayedarray)
-       ("r-dplyr" ,r-dplyr)
-       ("r-ggally" ,r-ggally)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-hexbin" ,r-hexbin)
-       ("r-hmisc" ,r-hmisc)
-       ("r-htmlwidgets" ,r-htmlwidgets)
-       ("r-plotly" ,r-plotly)
-       ("r-plyr" ,r-plyr)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-reshape" ,r-reshape)
-       ("r-shiny" ,r-shiny)
-       ("r-shinycssloaders" ,r-shinycssloaders)
-       ("r-shinydashboard" ,r-shinydashboard)
-       ("r-stringr" ,r-stringr)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-tidyr" ,r-tidyr)))
+     (list r-delayedarray
+           r-dplyr
+           r-ggally
+           r-ggplot2
+           r-gridextra
+           r-hexbin
+           r-hmisc
+           r-htmlwidgets
+           r-plotly
+           r-plyr
+           r-rcolorbrewer
+           r-reshape
+           r-shiny
+           r-shinycssloaders
+           r-shinydashboard
+           r-stringr
+           r-summarizedexperiment
+           r-tidyr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/lindsayrutter/bigPint")
     (synopsis "Big multivariate data plotted interactively")
     (description
@@ -11421,32 +11783,34 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
 (define-public r-chemminer
   (package
     (name "r-chemminer")
-    (version "3.44.0")
+    (version "3.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChemmineR" version))
        (sha256
         (base32
-         "1z59npqk7hnqzhjdnry6lfqlyxfzwqprp7bmbdzs4rp22pzcv1v8"))))
+         "069xd7if7fs69afmamgl6wrkzpnk97ic6z5ix4vvlzkb078dm0p8"))))
     (properties `((upstream-name . "ChemmineR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-base64enc" ,r-base64enc)
-       ("r-bh" ,r-bh)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-dbi" ,r-dbi)
-       ("r-digest" ,r-digest)
-       ("r-dt" ,r-dt)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-png" ,r-png)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rjson" ,r-rjson)
-       ("r-rsvg" ,r-rsvg)))
+     (list r-base64enc
+           r-bh
+           r-biocgenerics
+           r-dbi
+           r-digest
+           r-dt
+           r-ggplot2
+           r-gridextra
+           r-jsonlite
+           r-png
+           r-rcpp
+           r-rcurl
+           r-rjson
+           r-rsvg
+           r-stringi))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/girke-lab/ChemmineR")
     (synopsis "Cheminformatics toolkit for R")
     (description
@@ -11459,29 +11823,58 @@ visualization functions for compound clustering results and chemical
 structures.")
     (license license:artistic2.0)))
 
+(define-public r-fmcsr
+  (package
+    (name "r-fmcsr")
+    (version "1.36.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "fmcsR" version))
+        (sha256
+          (base32 "0mshslfj7jsix1yc03s54spbbi56zspic49kfsjfv8npikj1i5w0"))))
+    (properties `((upstream-name . "fmcsR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics r-chemminer r-runit))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/girke-lab/fmcsR")
+    (synopsis "Mismatch tolerant maximum common substructure searching")
+    (description
+     "The fmcsR package introduces an efficient @dfn{maximum common
+substructure} (MCS) algorithms combined with a novel matching strategy that
+allows for atom and/or bond mismatches in the substructures shared among two
+small molecules.  The resulting flexible MCSs (FMCSs) are often larger than
+strict MCSs, resulting in the identification of more common features in their
+source structures, as well as a higher sensitivity in finding compounds with
+weak structural similarities.  The fmcsR package provides several utilities to
+use the FMCS algorithm for pairwise compound comparisons, structure similarity
+searching and clustering.")
+    (license license:artistic2.0)))
+
 (define-public r-bioassayr
   (package
     (name "r-bioassayr")
-    (version "1.30.0")
+    (version "1.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioassayR" version))
        (sha256
         (base32
-         "1mlv80w8a7l8cii3dfqvanvh0qdqvcg8c1iiq4xlyvkjxfs64ka1"))))
+         "0pa8d7p9asp36wddkg779i3b9m12rxik56c54bmclnammr0cz89i"))))
     (properties `((upstream-name . "bioassayR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-chemminer" ,r-chemminer)
-       ("r-dbi" ,r-dbi)
-       ("r-matrix" ,r-matrix)
-       ("r-rjson" ,r-rjson)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-xml" ,r-xml)))
+     (list r-biocgenerics
+           r-chemminer
+           r-dbi
+           r-matrix
+           r-rjson
+           r-rsqlite
+           r-xml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/girke-lab/bioassayR")
     (synopsis "Cross-target analysis of small molecule bioactivity")
     (description
@@ -11497,23 +11890,20 @@ available bioactivity data.")
 (define-public r-biobroom
   (package
     (name "r-biobroom")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobroom" version))
        (sha256
         (base32
-         "1ybyhmrcvj6k1laxw9bc8jbn533frkzh9k8kl1ibd5pi368rfqzn"))))
+         "034gbywrscv23kk1qnk7sc7dxdckmf60wh29fz65v1n28mkf180r"))))
     (properties `((upstream-name . "biobroom")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-broom" ,r-broom)
-       ("r-dplyr" ,r-dplyr)
-       ("r-tidyr" ,r-tidyr)))
+     (list r-biobase r-broom r-dplyr r-tidyr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/StoreyLab/biobroom")
     (synopsis "Turn Bioconductor objects into tidy data frames")
     (description
@@ -11529,24 +11919,18 @@ visualize bioinformatics analyses.")
 (define-public r-graphite
   (package
     (name "r-graphite")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "graphite" version))
        (sha256
         (base32
-         "11bgz6951nfygxp3fm0190gf2bb5zplis1bc0am4757liw4qybhf"))))
+         "0wmdv4j6dinszxwpz2jddshkh1ahbhm2fxh6vhjsk4grw38i1lfr"))))
     (properties `((upstream-name . "graphite")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-checkmate" ,r-checkmate)
-       ("r-graph" ,r-graph)
-       ("r-httr" ,r-httr)
-       ("r-rappdirs" ,r-rappdirs)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-annotationdbi r-checkmate r-graph r-httr r-rappdirs))
     (home-page "https://bioconductor.org/packages/graphite/")
     (synopsis "Networks from pathway databases")
     (description
@@ -11558,27 +11942,27 @@ symbols).")
 (define-public r-reactomepa
   (package
     (name "r-reactomepa")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReactomePA" version))
        (sha256
         (base32
-         "1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf"))))
+         "1f4kd5cql7knnqaq3ba48kkypw8p60lkfdsnpqxcabdj30gqp55b"))))
     (properties `((upstream-name . "ReactomePA")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-dose" ,r-dose)
-       ("r-enrichplot" ,r-enrichplot)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggraph" ,r-ggraph)
-       ("r-graphite" ,r-graphite)
-       ("r-igraph" ,r-igraph)
-       ("r-reactome-db" ,r-reactome-db)))
+     (list r-annotationdbi
+           r-dose
+           r-enrichplot
+           r-ggplot2
+           r-ggraph
+           r-graphite
+           r-igraph
+           r-reactome-db))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://guangchuangyu.github.io/software/ReactomePA")
     (synopsis "Reactome pathway analysis")
     (description
@@ -11590,20 +11974,18 @@ enrichment analysis and several functions for visualization.")
 (define-public r-ebarrays
   (package
     (name "r-ebarrays")
-    (version "2.56.0")
+    (version "2.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBarrays" version))
        (sha256
         (base32
-         "1k1kl0m7wzaqpv7i20pfav2a6jf93bhri4w7qdikmvkf011n9422"))))
+         "10dw6c93rmpknzf4cnhw3y7lb27q4xq7x7wirl2a7qywdj0yj2g6"))))
     (properties `((upstream-name . "EBarrays")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-cluster" ,r-cluster)
-       ("r-lattice" ,r-lattice)))
+     (list r-biobase r-cluster r-lattice))
     (home-page "https://bioconductor.org/packages/EBarrays/")
     (synopsis "Gene clustering and differential expression identification")
     (description
@@ -11625,7 +12007,7 @@ microarray data.")
     (properties
      `((upstream-name . "BiocCaseStudies")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-biobase" ,r-biobase)))
+    (propagated-inputs (list r-biobase))
     (home-page "https://bioconductor.org/packages/BiocCaseStudies")
     (synopsis "Support for the case studies monograph")
     (description
@@ -11636,27 +12018,27 @@ monograph.")
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "1h0l5w33c9jpc20pynq634qmx8jbfa802d7jslmf4haljmrxm4a1"))))
+                "0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-codetools" ,r-codetools)
-       ("r-graph" ,r-graph)
-       ("r-httr" ,r-httr)
-       ("r-knitr" ,r-knitr)
-       ("r-optparse" ,r-optparse)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biocviews" ,r-biocviews)
-       ("r-stringdist" ,r-stringdist)))
+     (list r-codetools
+           r-graph
+           r-httr
+           r-knitr
+           r-optparse
+           r-biocmanager
+           r-biocviews
+           r-stringdist))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiocCheck")
     (synopsis "Executes Bioconductor-specific package checks")
     (description "This package contains tools to perform additional quality
@@ -11666,21 +12048,18 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
 (define-public r-biocgraph
   (package
     (name "r-biocgraph")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocGraph" version))
        (sha256
         (base32
-         "12bmj9kdlylp02cfwviak7y323ndccl2694rvi4cdg4vsx7v3ya3"))))
+         "0c7r0c1kx22dlwi6d1ldbkkbf53yi0p3vmgbwzrbkn3cina7bcxq"))))
     (properties `((upstream-name . "biocGraph")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-geneplotter" ,r-geneplotter)
-       ("r-graph" ,r-graph)
-       ("r-rgraphviz" ,r-rgraphviz)))
+     (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
     (home-page "https://bioconductor.org/packages/biocGraph/")
     (synopsis "Graph examples and use cases in Bioinformatics")
     (description
@@ -11691,24 +12070,20 @@ different graph related packages produced by Bioconductor.")
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-    (version "2.20.2")
+    (version "2.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "0p2wdq5vrx63ndghl9ww428z2lwnv5y88xmcr51by2g6vcj3brcf"))))
+                "0xx6xr01sb5wig94515zxgw24r9fv0g962ajy87741civhq32lbd"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocmanager" ,r-biocmanager)
-       ("r-bookdown" ,r-bookdown)
-       ("r-knitr" ,r-knitr)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("r-yaml" ,r-yaml)))
+     (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiocStyle")
     (synopsis "Bioconductor formatting styles")
     (description "This package provides standard formatting styles for
@@ -11719,24 +12094,24 @@ functionality.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.60.0")
+    (version "1.62.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "0pc5ll59vm8a9s1nrdc7p9wk11a52rrz669fsrrqd8qapa8p6wfd"))))
+                "1v6himzp546dpb990vv0nlya21w8x2x30137rsmahjzg942nzs9r"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-graph" ,r-graph)
-       ("r-rbgl" ,r-rbgl)
-       ("r-rcurl" ,r-rcurl)
-       ("r-xml" ,r-xml)
-       ("r-runit" ,r-runit)))
+     (list r-biobase
+           r-biocmanager
+           r-graph
+           r-rbgl
+           r-rcurl
+           r-xml
+           r-runit))
     (home-page "https://bioconductor.org/packages/biocViews")
     (synopsis "Bioconductor package categorization helper")
     (description "The purpose of biocViews is to create HTML pages that
@@ -11747,26 +12122,26 @@ also known as views, in a controlled vocabulary.")
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ExperimentHub" version))
        (sha256
         (base32
-         "1mzmw3100lf33yhz27nbxncrjk5bprlackrjcwf8xdhcaidg40p4"))))
+         "15las4qmqvrn81hczxa3ylikqh54kp1lg9r8rcyfvrx5l0kgwlfq"))))
     (properties `((upstream-name . "ExperimentHub")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationhub" ,r-annotationhub)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-curl" ,r-curl)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-annotationhub
+           r-biocfilecache
+           r-biocgenerics
+           r-biocmanager
+           r-curl
+           r-rappdirs
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/ExperimentHub/")
     (synopsis "Client to access ExperimentHub resources")
     (description
@@ -11781,24 +12156,24 @@ access.")
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "1h63vg1iskw79ijg5h1b9097ams8pp3kvnlawlfci6xfli07xpkj"))))
+         "1jcj29df4prknqwbydca1jb9w6njacjhwwk9jp0r5mvb88xrm60s"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-mass" ,r-mass)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-iranges
+           r-mass
+           r-rtracklayer
+           r-s4vectors))
     (home-page "https://github.com/Kraus-Lab/groHMM")
     (synopsis "GRO-seq analysis pipeline")
     (description
@@ -11808,27 +12183,27 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51"))))
+         "1h3b8vqlbd04amjprxd1814zksdrbi01a0xn3906vkbqi43hfyn9"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-tidyr" ,r-tidyr)))
+     (list r-biobase
+           r-biocgenerics
+           r-genomicranges
+           r-iranges
+           r-s4vectors
+           r-summarizedexperiment
+           r-tidyr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://waldronlab.io/MultiAssayExperiment/")
     (synopsis "Integration of multi-omics experiments in Bioconductor")
     (description
@@ -11843,41 +12218,41 @@ rownames.")
 (define-public r-bioconcotk
   (package
     (name "r-bioconcotk")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocOncoTK" version))
        (sha256
         (base32
-         "1ix09a39z7y2cj0y8qsd66ka8a8y8q79w08l4jv1yhhn9h4va89s"))))
+         "1h5s6wbc5n5x5d28rynxpcmaklxdhf72g9gg9fy8cg77niipvxd9"))))
     (properties `((upstream-name . "BiocOncoTK")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bigrquery" ,r-bigrquery)
-       ("r-car" ,r-car)
-       ("r-complexheatmap" ,r-complexheatmap)
-       ("r-curatedtcgadata" ,r-curatedtcgadata)
-       ("r-dbi" ,r-dbi)
-       ("r-dplyr" ,r-dplyr)
-       ("r-dt" ,r-dt)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggpubr" ,r-ggpubr)
-       ("r-graph" ,r-graph)
-       ("r-httr" ,r-httr)
-       ("r-iranges" ,r-iranges)
-       ("r-magrittr" ,r-magrittr)
-       ("r-plyr" ,r-plyr)
-       ("r-rgraphviz" ,r-rgraphviz)
-       ("r-rjson" ,r-rjson)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-shiny" ,r-shiny)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-bigrquery
+           r-car
+           r-complexheatmap
+           r-curatedtcgadata
+           r-dbi
+           r-dplyr
+           r-dt
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-ggpubr
+           r-graph
+           r-httr
+           r-iranges
+           r-magrittr
+           r-plyr
+           r-rgraphviz
+           r-rjson
+           r-s4vectors
+           r-scales
+           r-shiny
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiocOncoTK")
     (synopsis "Bioconductor components for general cancer genomics")
     (description
@@ -11888,22 +12263,20 @@ tools for genome-scale analysis of cancer studies.")
 (define-public r-biocor
   (package
     (name "r-biocor")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioCor" version))
        (sha256
         (base32
-         "135rga7mwpzy8ypvriqpbmlh9l5yf61s9s1sa9615qfab14jh06b"))))
+         "0ii4g7438lb34ykidkbxw3v3k289k662rgbgayf9gak5avpkb2cq"))))
     (properties `((upstream-name . "BioCor")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-gseabase" ,r-gseabase)
-       ("r-matrix" ,r-matrix)))
+     (list r-biocparallel r-gseabase r-matrix))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://llrs.github.io/BioCor/")
     (synopsis "Functional similarities")
     (description
@@ -11917,41 +12290,41 @@ gene selection, testing relationships, and so on.")
 (define-public r-biocpkgtools
   (package
     (name "r-biocpkgtools")
-    (version "1.10.2")
+    (version "1.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocPkgTools" version))
        (sha256
         (base32
-         "1sfp1nxlwbbbpx2iwvyk9p10jdy2vxhgn2b5fy5blayzjjlb3d80"))))
+         "1yz2sgx4xrnw22k3d6q6hkj213bnbb4hbr5ymxnmjnsz551s75ny"))))
     (properties `((upstream-name . "BiocPkgTools")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocfilecache" ,r-biocfilecache)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biocviews" ,r-biocviews)
-       ("r-dplyr" ,r-dplyr)
-       ("r-dt" ,r-dt)
-       ("r-gh" ,r-gh)
-       ("r-graph" ,r-graph)
-       ("r-htmltools" ,r-htmltools)
-       ("r-htmlwidgets" ,r-htmlwidgets)
-       ("r-httr" ,r-httr)
-       ("r-igraph" ,r-igraph)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-magrittr" ,r-magrittr)
-       ("r-rbgl" ,r-rbgl)
-       ("r-readr" ,r-readr)
-       ("r-rlang" ,r-rlang)
-       ("r-rvest" ,r-rvest)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)
-       ("r-tidyselect" ,r-tidyselect)
-       ("r-xml2" ,r-xml2)))
+     (list r-biocfilecache
+           r-biocmanager
+           r-biocviews
+           r-dplyr
+           r-dt
+           r-gh
+           r-graph
+           r-htmltools
+           r-htmlwidgets
+           r-httr
+           r-igraph
+           r-jsonlite
+           r-magrittr
+           r-rbgl
+           r-readr
+           r-rlang
+           r-rvest
+           r-stringr
+           r-tibble
+           r-tidyr
+           r-tidyselect
+           r-xml2))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/seandavi/BiocPkgTools")
     (synopsis "Collection of tools for learning about Bioconductor packages")
     (description
@@ -11965,29 +12338,29 @@ analytics on packages.")
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.6.1")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "0nmrg9cgq8l9w467y364jghnvym05abpj8pyj90grmrib2xc5sj2"))))
+         "1x5ar9byr85iap2x6y66j31fi17wr31awx1gl3z01sckp0dldx6w"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocio" ,r-biocio)
-       ("r-dplyr" ,r-dplyr)
-       ("r-keggrest" ,r-keggrest)
-       ("r-ontologyindex" ,r-ontologyindex)
-       ("r-plyr" ,r-plyr)
-       ("r-rlang" ,r-rlang)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)))
+     (list r-annotationdbi
+           r-biocio
+           r-dplyr
+           r-keggrest
+           r-ontologyindex
+           r-plyr
+           r-rlang
+           r-s4vectors
+           r-tibble
+           r-tidyr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page
      "https://bioconductor.org/packages/BiocSet")
     (synopsis
@@ -12003,29 +12376,29 @@ accessing web references for elements/sets are also available in BiocSet.")
 (define-public r-biocworkflowtools
   (package
     (name "r-biocworkflowtools")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocWorkflowTools" version))
        (sha256
         (base32
-         "1a32bwgnxaw0gv2gij2p4rm0a6l06jjhidvfz2v4k900pz1w79av"))))
+         "1j9s8w5y8savcmh70npkanxacq1kipxnwk1wsiw5hwnp1p13ldaa"))))
     (properties
      `((upstream-name . "BiocWorkflowTools")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocstyle" ,r-biocstyle)
-       ("r-bookdown" ,r-bookdown)
-       ("r-git2r" ,r-git2r)
-       ("r-httr" ,r-httr)
-       ("r-knitr" ,r-knitr)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("r-rstudioapi" ,r-rstudioapi)
-       ("r-stringr" ,r-stringr)
-       ("r-usethis" ,r-usethis)))
+     (list r-biocstyle
+           r-bookdown
+           r-git2r
+           r-httr
+           r-knitr
+           r-rmarkdown
+           r-rstudioapi
+           r-stringr
+           r-usethis))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
     (synopsis "Tools to aid the development of Bioconductor Workflow packages")
     (description
@@ -12036,19 +12409,18 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
 (define-public r-biodist
   (package
     (name "r-biodist")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioDist" version))
        (sha256
         (base32
-         "1y1x9q9aa76gbhsyfn638rxp5icjvq30fv3a4205xh7g5jwlf6yw"))))
+         "0y35c9sdq5x4q64ip0wgqz59mh01l71k1pp6n8vqbr667nwg0gdp"))))
     (properties `((upstream-name . "bioDist")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-kernsmooth" ,r-kernsmooth)))
+     (list r-biobase r-kernsmooth))
     (home-page "https://bioconductor.org/packages/bioDist/")
     (synopsis "Different distance measures")
     (description
@@ -12059,32 +12431,32 @@ distance measures.")
 (define-public r-pcatools
   (package
     (name "r-pcatools")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "PCAtools" version))
        (sha256
         (base32
-         "11idi9fwvyhkakbm63qxcdhkany8gbskis04z0p5a39lppq8ks31"))))
+         "10kfhsxhsjpzal3yvcqg769h5fz99cqqjq217cj9jip3jfh2m2h4"))))
     (properties `((upstream-name . "PCAtools")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-bh" ,r-bh)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biocsingular" ,r-biocsingular)
-       ("r-cowplot" ,r-cowplot)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-dqrng" ,r-dqrng)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggrepel" ,r-ggrepel)
-       ("r-lattice" ,r-lattice)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-reshape2" ,r-reshape2)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-beachmat
+           r-bh
+           r-biocparallel
+           r-biocsingular
+           r-cowplot
+           r-delayedarray
+           r-delayedmatrixstats
+           r-dqrng
+           r-ggplot2
+           r-ggrepel
+           r-lattice
+           r-matrix
+           r-rcpp
+           r-reshape2))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/kevinblighe/PCAtools")
     (synopsis "PCAtools: everything Principal Components Analysis")
     (description
@@ -12105,23 +12477,19 @@ dimensional mass cytometry data.")
 (define-public r-rgreat
   (package
     (name "r-rgreat")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGREAT" version))
        (sha256
         (base32
-         "0ads9c9i8b39wvjih057zlyivj8zpsqjxf6r97yflz4sbi1jmcji"))))
+         "0kr61mhxp9phn1136fci450zwfhsipchmlm8d5rgib4lh0zbxrhl"))))
     (properties `((upstream-name . "rGREAT")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-genomicranges" ,r-genomicranges)
-       ("r-getoptlong" ,r-getoptlong)
-       ("r-iranges" ,r-iranges)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rjson" ,r-rjson)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/jokergoo/rGREAT")
     (synopsis "Client for GREAT analysis")
     (description
@@ -12133,28 +12501,28 @@ user's input and automatically retrieving results from GREAT web server.")
 (define-public r-m3c
   (package
     (name "r-m3c")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "M3C" version))
        (sha256
         (base32
-         "17gj4haa4ywc6bmppm342jzppl3inqa94235yspikij6c098vrmc"))))
+         "0jsql5wd58hs5mnn9wq5b4kl3z57y6amykirfb3k047zpyi8ijnh"))))
     (properties `((upstream-name . "M3C")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-cluster" ,r-cluster)
-       ("r-corpcor" ,r-corpcor)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dosnow" ,r-dosnow)
-       ("r-foreach" ,r-foreach)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixcalc" ,r-matrixcalc)
-       ("r-rtsne" ,r-rtsne)
-       ("r-umap" ,r-umap)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-cluster
+           r-corpcor
+           r-doparallel
+           r-dosnow
+           r-foreach
+           r-ggplot2
+           r-matrix
+           r-matrixcalc
+           r-rtsne
+           r-umap))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/M3C")
     (synopsis "Monte Carlo reference-based consensus clustering")
     (description
@@ -12166,18 +12534,18 @@ hypothesis @code{K=1}.")
 (define-public r-icens
   (package
     (name "r-icens")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Icens" version))
        (sha256
         (base32
-         "1rzgwxx4w2bqsaz0xmkhi4w9zsxgms80xf59zg1xp1camyhaihlz"))))
+         "08jd7g28mazvwd3qbq8y26czmkz45avp4vy8l7i5d6qajwzqzgzs"))))
     (properties `((upstream-name . "Icens")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-survival" ,r-survival)))
+     (list r-survival))
     (home-page "https://bioconductor.org/packages/Icens")
     (synopsis "NPMLE for censored and truncated data")
     (description
@@ -12191,21 +12559,18 @@ truncated data.")
 (define-public r-interval
   (package
     (name "r-interval")
-    (version "1.1-0.7")
+    (version "1.1-0.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "interval" version))
        (sha256
         (base32
-         "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
+         "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
     (properties `((upstream-name . "interval")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-icens" ,r-icens)
-       ("r-mlecens" ,r-mlecens)
-       ("r-perm" ,r-perm)
-       ("r-survival" ,r-survival)))
+     (list r-icens r-mlecens r-perm r-survival))
     (home-page "https://cran.r-project.org/web/packages/interval/")
     (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
     (description
@@ -12229,11 +12594,7 @@ plot them, and perform logrank or Wilcoxon type tests.")
     (properties `((upstream-name . "FHtest")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-interval" ,r-interval)
-       ("r-kmsurv" ,r-kmsurv)
-       ("r-mass" ,r-mass)
-       ("r-perm" ,r-perm)
-       ("r-survival" ,r-survival)))
+     (list r-interval r-kmsurv r-mass r-perm r-survival))
     (home-page "https://cran.r-project.org/web/packages/FHtest/")
     (synopsis "Tests for survival data based on the Fleming-Harrington class")
     (description
@@ -12262,23 +12623,23 @@ with:
     (properties `((upstream-name . "FourCSeq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biostrings" ,r-biostrings)
-       ("r-deseq2" ,r-deseq2)
-       ("r-fda" ,r-fda)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggbio" ,r-ggbio)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gtools" ,r-gtools)
-       ("r-lsd" ,r-lsd)
-       ("r-matrix" ,r-matrix)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-biobase
+           r-biostrings
+           r-deseq2
+           r-fda
+           r-genomicalignments
+           r-genomicranges
+           r-ggbio
+           r-ggplot2
+           r-gtools
+           r-lsd
+           r-matrix
+           r-reshape2
+           r-rsamtools
+           r-rtracklayer
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page
      "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
     (synopsis "Analysis of multiplexed 4C sequencing data")
@@ -12296,14 +12657,14 @@ generated.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "17a00blz4kvhmsk92bp5alj9kdpy7h1id7nk4vqxakhkb2jabr20"))))
+         "1i93vdqa6pwzamiryp3lv6cyvhx9shs01is0q6vbmdvcbii2vf3x"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -12317,18 +12678,18 @@ routines.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.30.1")
+    (version "0.32.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "103sw0fmmm4f3hprrsn7dwg0kmmr9mcmb46dcwwb6p5np0al2sfx"))))
+                "0wp29v41f9cf6khq2ww0f63nsq6219l1ycajzdqp3a2xda734ncw"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)))
+     (list r-biocgenerics))
     (home-page "https://bioconductor.org/packages/S4Vectors")
     (synopsis "S4 implementation of vectors and lists")
     (description
@@ -12357,18 +12718,18 @@ S4Vectors package itself.")
     (properties `((upstream-name . "WGCNA")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dynamictreecut" ,r-dynamictreecut)
-       ("r-fastcluster" ,r-fastcluster)
-       ("r-foreach" ,r-foreach)
-       ("r-go-db" ,r-go-db)
-       ("r-hmisc" ,r-hmisc)
-       ("r-impute" ,r-impute)
-       ("r-rcpp" ,r-rcpp)
-       ("r-survival" ,r-survival)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-preprocesscore" ,r-preprocesscore)))
+     (list r-annotationdbi
+           r-doparallel
+           r-dynamictreecut
+           r-fastcluster
+           r-foreach
+           r-go-db
+           r-hmisc
+           r-impute
+           r-rcpp
+           r-survival
+           r-matrixstats
+           r-preprocesscore))
     (home-page
      "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
     (synopsis "Weighted correlation network analysis")
@@ -12384,14 +12745,14 @@ data manipulation and visualization.")
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-    (version "2.36.0")
+    (version "2.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rgraphviz" version))
        (sha256
         (base32
-         "0d0xq1vgr4b165cn4wg7zmfjyc1d9ir4amgs196j4cgrhpmrnl8s"))))
+         "0fyv1ybpahkwz3fawzxgxfnshi8y7c18262rgdmqwdl5662vv1p7"))))
     (properties `((upstream-name . "Rgraphviz")))
     (build-system r-build-system)
     (arguments
@@ -12407,11 +12768,11 @@ data manipulation and visualization.")
     ;; FIXME: Rgraphviz bundles the sources of an older variant of
     ;; graphviz.  It does not build with the latest version of graphviz, so
     ;; we do not add graphviz to the inputs.
-    (inputs `(("zlib" ,zlib)))
+    (inputs (list zlib))
     (propagated-inputs
-     `(("r-graph" ,r-graph)))
+     (list r-graph))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     (list pkg-config))
     (home-page "https://bioconductor.org/packages/Rgraphviz")
     (synopsis "Plotting capabilities for R graph objects")
     (description
@@ -12422,21 +12783,19 @@ objects from the @code{graph} package.")
 (define-public r-fithic
   (package
     (name "r-fithic")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "FitHiC" version))
               (sha256
                (base32
-                "1p8a6lis5yswaj647bjw89harlarnsxmvjzz63fn1l6gxrwhh8bx"))))
+                "0a3d2bxp98lmbf3i864zgfwxwvxyqfcrh75z9yz7ra7y44pkjr4y"))))
     (properties `((upstream-name . "FitHiC")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-fdrtool" ,r-fdrtool)
-       ("r-rcpp" ,r-rcpp)))
+     (list r-data-table r-fdrtool r-rcpp))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/FitHiC")
     (synopsis "Confidence estimation for intra-chromosomal contact maps")
     (description
@@ -12448,23 +12807,23 @@ assays such as Hi-C.")
 (define-public r-hitc
   (package
     (name "r-hitc")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "HiTC" version))
               (sha256
                (base32
-                "0s3kfqs3zlmq61hxdmxpmi9gfs9w3byckw7xzp1hrhdbsl46yvgq"))))
+                "1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx"))))
     (properties `((upstream-name . "HiTC")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rtracklayer" ,r-rtracklayer)))
+     (list r-biostrings
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-matrix
+           r-rcolorbrewer
+           r-rtracklayer))
     (home-page "https://bioconductor.org/packages/HiTC")
     (synopsis "High throughput chromosome conformation capture analysis")
     (description
@@ -12477,27 +12836,27 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.20.0")
+    (version "1.22.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1718hplz5qlbwxwb87509bl7lir9kilvn1s7p2haz551pg48zvrc"))))
+         "1al4a88pgdl7hfhphsnwl1gg1c1kmw37wcdr4v4pfsw5l8ff7nx4"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs
-     `(("zlib" ,zlib)))
+     (list zlib))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-rhdf5" ,r-rhdf5)
-       ("r-rhdf5filters" ,r-rhdf5filters)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocgenerics
+           r-delayedarray
+           r-iranges
+           r-matrix
+           r-rhdf5
+           r-rhdf5filters
+           r-rhdf5lib
+           r-s4vectors))
     (home-page "https://bioconductor.org/packages/HDF5Array")
     (synopsis "HDF5 back end for DelayedArray objects")
     (description "This package provides an array-like container for convenient
@@ -12508,14 +12867,14 @@ block processing.")
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.14.2")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "1cwynbcaaxmbh45fc0d264liqdj0wbjlj7k2bsq3qfjbnh6kkam5"))
+         "0yly9s3wdnhd9ci2jxfkql38ibv35yzs38a6g6ashbg1m5kgwd9p"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -12577,8 +12936,7 @@ block processing.")
                  (("cp \"\\$\\{SZIP_LIB\\}.*") "")
                  (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
     (propagated-inputs
-     `(("hdf5" ,hdf5-1.10)
-       ("zlib" ,zlib)))
+     (list hdf5-1.10 zlib))
     (native-inputs
      `(("hdf5-source" ,(package-source hdf5-1.10))
        ("r-knitr" ,r-knitr)))
@@ -12591,22 +12949,19 @@ packages.")
 (define-public r-beachmat
   (package
     (name "r-beachmat")
-    (version "2.8.1")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "beachmat" version))
        (sha256
         (base32
-         "06bpfpddsl49csxrs8hlx5pv0absc2wdcparchf8qqaqydazwci2"))))
+         "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)))
+     (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/beachmat")
     (synopsis "Compiling Bioconductor to handle each matrix type")
     (description "This package provides a consistent C++ class interface for a
@@ -12620,38 +12975,38 @@ matrices.")
 (define-public r-cner
   (package
     (name "r-cner")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CNEr" version))
        (sha256
-        (base32 "13w0gsfm7k29dp5nb0c9sb2ix506ph6dixsjis6xxcz6acq7lg2k"))))
+        (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2"))))
     (properties `((upstream-name . "CNEr")))
     (build-system r-build-system)
-    (inputs `(("zlib" ,zlib)))
+    (inputs (list zlib))
     (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-go-db" ,r-go-db)
-       ("r-iranges" ,r-iranges)
-       ("r-keggrest" ,r-keggrest)
-       ("r-powerlaw" ,r-powerlaw)
-       ("r-r-utils" ,r-r-utils)
-       ("r-readr" ,r-readr)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
+     (list r-annotate
+           r-biocgenerics
+           r-biostrings
+           r-dbi
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-go-db
+           r-iranges
+           r-keggrest
+           r-powerlaw
+           r-r-utils
+           r-readr
+           r-reshape2
+           r-rsqlite
+           r-rtracklayer
+           r-s4vectors
+           r-xvector))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/ge11232002/CNEr")
     (synopsis "CNE Detection and Visualization")
     (description
@@ -12668,38 +13023,38 @@ advanced visualization of sets of conserved noncoding elements.")
 (define-public r-tfbstools
   (package
     (name "r-tfbstools")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TFBSTools" version))
        (sha256
         (base32
-         "1avgjv2nyr28cla0z9dvh3v0hr1f561sz2as1k53a42irbjk0var"))))
+         "0j5gv145fczzdspwhbywlg47y05pgnkra9jg7bn4wa1k0cf5pr9g"))))
     (properties `((upstream-name . "TFBSTools")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-catools" ,r-catools)
-       ("r-cner" ,r-cner)
-       ("r-dbi" ,r-dbi)
-       ("r-dirichletmultinomial" ,r-dirichletmultinomial)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gtools" ,r-gtools)
-       ("r-iranges" ,r-iranges)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-seqlogo" ,r-seqlogo)
-       ("r-tfmpvalue" ,r-tfmpvalue)
-       ("r-xml" ,r-xml)
-       ("r-xvector" ,r-xvector)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-bsgenome
+           r-catools
+           r-cner
+           r-dbi
+           r-dirichletmultinomial
+           r-genomeinfodb
+           r-genomicranges
+           r-gtools
+           r-iranges
+           r-rsqlite
+           r-rtracklayer
+           r-s4vectors
+           r-seqlogo
+           r-tfmpvalue
+           r-xml
+           r-xvector))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/ge11232002/TFBSTools")
     (synopsis "Transcription factor binding site (TFBS) analysis")
     (description
@@ -12711,33 +13066,57 @@ scan putative TFBS from sequence/alignment, query JASPAR database and
 provides a wrapper of de novo motif discovery software.")
     (license license:gpl2)))
 
+(define-public r-maftools
+  (package
+    (name "r-maftools")
+    (version "2.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "maftools" version))
+       (sha256
+        (base32 "1s8w3xwwigz803l81bs9cb2dbvvw5r9z8jjcav1rmh9wm8909nfd"))))
+    (properties `((upstream-name . "maftools")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-data-table r-rcolorbrewer r-rhtslib r-survival r-zlibbioc))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/PoisonAlien/maftools")
+    (synopsis "Summarize, analyze and visualize MAF files")
+    (description
+     "Analyze and visualize Mutation Annotation Format (MAF) files from large
+scale sequencing studies.  This package provides various functions to perform
+most commonly used analyses in cancer genomics and to create feature rich
+customizable visualzations with minimal effort.")
+    (license license:expat)))
+
 (define-public r-motifmatchr
   (package
     (name "r-motifmatchr")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifmatchr" version))
        (sha256
         (base32
-         "1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm"))))
+         "0f7j54zdn51h1gcn81vqs8avmschjwqprjcfpvsi00q4fna3fg7z"))))
     (properties `((upstream-name . "motifmatchr")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-tfbstools" ,r-tfbstools)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-biostrings
+           r-bsgenome
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-matrix
+           r-rcpp
+           r-rcpparmadillo
+           r-rsamtools
+           r-s4vectors
+           r-summarizedexperiment
+           r-tfbstools))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/motifmatchr")
     (synopsis "Fast motif matching in R")
     (description
@@ -12748,39 +13127,39 @@ This package wraps C++ code from the MOODS motif calling library.")
 (define-public r-chromvar
   (package
     (name "r-chromvar")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromVAR" version))
        (sha256
-        (base32 "1birmwvcvl2hb5ygbsb3wvbdfayqqs53j1bks46cbkq7ybigfyar"))))
+        (base32 "0ylsfr540l763bh010irbcavlskahyb1769pppimdgn22gyr3spk"))))
     (properties `((upstream-name . "chromVAR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-dt" ,r-dt)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-miniui" ,r-miniui)
-       ("r-nabor" ,r-nabor)
-       ("r-plotly" ,r-plotly)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtsne" ,r-rtsne)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-tfbstools" ,r-tfbstools)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-bsgenome
+           r-dt
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-matrix
+           r-miniui
+           r-nabor
+           r-plotly
+           r-rcolorbrewer
+           r-rcpp
+           r-rcpparmadillo
+           r-rsamtools
+           r-rtsne
+           r-s4vectors
+           r-shiny
+           r-summarizedexperiment
+           r-tfbstools))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
     (synopsis "Determine chromatin variation across regions")
     (description
@@ -12795,25 +13174,22 @@ sequence (@code{DNAse-seq}) experiments.")
 (define-public r-singlecellexperiment
   (package
     (name "r-singlecellexperiment")
-    (version "1.14.1")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleCellExperiment" version))
        (sha256
         (base32
-         "1bwdhx0ss0s8f4xdgwd7x48apn849x4dyb5hbyglcz31r5vh1qgz"))))
+         "01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39"))))
     (properties
      `((upstream-name . "SingleCellExperiment")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/SingleCellExperiment")
     (synopsis "S4 classes for single cell data")
     (description "This package defines an S4 class for storing data from
@@ -12823,32 +13199,64 @@ factors for each cell, along with the usual metadata for genes and
 libraries.")
     (license license:gpl3)))
 
+(define-public r-singler
+  (package
+    (name "r-singler")
+    (version "1.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "SingleR" version))
+       (sha256
+        (base32 "19lsn3cpghkhfbx4jqgbwwrnacrl7vj3r91ymd1gk02c9pn5dmci"))))
+    (properties `((upstream-name . "SingleR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-beachmat
+           r-biocneighbors
+           r-biocparallel
+           r-biocsingular
+           r-delayedarray
+           r-delayedmatrixstats
+           r-matrix
+           r-rcpp
+           r-s4vectors
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/LTLA/SingleR")
+    (synopsis "Reference-based single-cell RNA-seq annotation")
+    (description
+     "This package performs unbiased cell type recognition from single-cell
+RNA sequencing data, by leveraging reference transcriptomic datasets of pure
+cell types to infer the cell of origin of each single cell independently.")
+    (license license:gpl3)))
+
 (define-public r-scuttle
   (package
     (name "r-scuttle")
-    (version "1.2.1")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scuttle" version))
        (sha256
         (base32
-         "015k879gg2r39lp6mz26jwmysa56k0ial6v74zzmbi8hnz9zic3i"))))
+         "1dbdb6yc6wk01dljy1vy6f0lf44crc5rxxnc4bhjk8i4iljz8467"))))
     (properties `((upstream-name . "scuttle")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-beachmat
+           r-biocgenerics
+           r-biocparallel
+           r-delayedarray
+           r-delayedmatrixstats
+           r-genomicranges
+           r-matrix
+           r-rcpp
+           r-s4vectors
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/scuttle")
     (synopsis "Single-cell RNA-Seq analysis utilities")
     (description
@@ -12861,36 +13269,37 @@ of other packages.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.20.1")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "1046fgf93dda3y2z5ilrjdczz7klj67ag63p4p1h03965wpj9vfn"))))
+                "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocneighbors" ,r-biocneighbors)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biocsingular" ,r-biocsingular)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-ggbeeswarm" ,r-ggbeeswarm)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-matrix" ,r-matrix)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rlang" ,r-rlang)
-       ("r-rtsne" ,r-rtsne)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scuttle" ,r-scuttle)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-viridis" ,r-viridis)))
+     (list r-beachmat
+           r-biocgenerics
+           r-biocneighbors
+           r-biocparallel
+           r-biocsingular
+           r-delayedarray
+           r-delayedmatrixstats
+           r-ggbeeswarm
+           r-ggplot2
+           r-ggrepel
+           r-gridextra
+           r-matrix
+           r-rcolorbrewer
+           r-rlang
+           r-rtsne
+           r-s4vectors
+           r-scuttle
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-viridis))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/davismcc/scater")
     (synopsis "Single-cell analysis toolkit for gene expression data in R")
     (description "This package provides a collection of tools for doing
@@ -12901,38 +13310,38 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.20.1")
+    (version "1.22.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "0ilzp6ngw9pq88gk79iic2zxfh5jaic6lnq3xfwc9a269bjylff0"))))
+         "06lcxya6rpa8dv0il7m7fwyx0ci1y1jn16ff5lmvzf2mnr6q7lic"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-bh" ,r-bh)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biocsingular" ,r-biocsingular)
-       ("r-bluster" ,r-bluster)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-dqrng" ,r-dqrng)
-       ("r-edger" ,r-edger)
-       ("r-igraph" ,r-igraph)
-       ("r-limma" ,r-limma)
-       ("r-matrix" ,r-matrix)
-       ("r-metapod" ,r-metapod)
-       ("r-rcpp" ,r-rcpp)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scuttle" ,r-scuttle)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-statmod" ,r-statmod)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-beachmat
+           r-bh
+           r-biocgenerics
+           r-biocparallel
+           r-biocsingular
+           r-bluster
+           r-delayedarray
+           r-delayedmatrixstats
+           r-dqrng
+           r-edger
+           r-igraph
+           r-limma
+           r-matrix
+           r-metapod
+           r-rcpp
+           r-s4vectors
+           r-scuttle
+           r-singlecellexperiment
+           r-statmod
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/scran")
     (synopsis "Methods for single-cell RNA-Seq data analysis")
     (description "This package implements a variety of low-level analyses of
@@ -12944,23 +13353,20 @@ variable and significantly correlated genes.")
 (define-public r-sparsematrixstats
   (package
     (name "r-sparsematrixstats")
-    (version "1.4.2")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sparseMatrixStats" version))
        (sha256
         (base32
-         "0b22kzg751zlkcbs8pi0bcqrsj3imsg35qfvxfrqb7gav7qznc8v"))))
+         "0ifqj4a6mn4749sr62gq3dwd6mmbbzdx5mh5b5663vcgl1kw96x1"))))
     (properties
      `((upstream-name . "sparseMatrixStats")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-matrix" ,r-matrix)
-       ("r-matrixgenerics" ,r-matrixgenerics)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rcpp" ,r-rcpp)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
     (synopsis "Summary statistics for rows and columns of sparse matrices")
     (description
@@ -12972,27 +13378,27 @@ data in the column sparse format.")
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.14.3")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "1zxs2wjnsq9w1cl4andsd7y9xsdnl1an55khw9viaq758m7hhbcn"))))
+         "1pqwkk39rfhcnhmgchk0gfmm4jgasl19yq0nhhwsfj45y2vk6kjk"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-delayedarray" ,r-delayedarray)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixgenerics" ,r-matrixgenerics)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-sparsematrixstats" ,r-sparsematrixstats)))
+     (list r-delayedarray
+           r-iranges
+           r-matrix
+           r-matrixgenerics
+           r-matrixstats
+           r-s4vectors
+           r-sparsematrixstats))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
     (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
     (description
@@ -13008,23 +13414,20 @@ memory usage and processing time is minimized.")
 (define-public r-mscoreutils
   (package
     (name "r-mscoreutils")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsCoreUtils" version))
        (sha256
         (base32
-         "13g8a726vsyjs6m1kd42vf8avdnmhykxhl6z3j2njzkp2jg17pd8"))))
+         "1w8d1v2r3plwwcz23zhbpvklhapf2a6x3xmglyh4sh6sy9ynkgrv"))))
     (properties `((upstream-name . "MsCoreUtils")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-clue" ,r-clue)
-       ("r-mass" ,r-mass)
-       ("r-rcpp" ,r-rcpp)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-clue r-mass r-rcpp r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
     (synopsis "Core utils for mass spectrometry data")
     (description
@@ -13037,24 +13440,53 @@ well as misc helper functions, that are used across high-level data structure
 within the R for Mass Spectrometry packages.")
     (license license:artistic2.0)))
 
+(define-public r-msfeatures
+  (package
+    (name "r-msfeatures")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MsFeatures" version))
+       (sha256
+        (base32 "020ifrijlzdd3qk4bhd9z4knj5d87ildrkl3wcmxvwkvs9rbh8rq"))))
+    (properties `((upstream-name . "MsFeatures")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-mscoreutils r-protgenerics r-summarizedexperiment))
+    (native-inputs
+     (list r-knitr))
+    (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
+    (synopsis "Functionality for mass spectrometry features")
+    (description
+     "The MsFeature package defines functionality for Mass Spectrometry
+features.  This includes functions to group (LC-MS) features based on some of
+their properties, such as retention time (coeluting features), or correlation
+of signals across samples.  This package hence can be used to group features, and
+its results can be used as an input for the @code{QFeatures} package which
+allows aggregating abundance levels of features within each group.  This
+package defines concepts and functions for base and common data types,
+implementations for more specific data types are expected to be implemented in
+the respective packages (such as e.g. @code{xcms}).")
+    (license license:artistic2.0)))
+
 (define-public r-biocio
   (package
     (name "r-biocio")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "BiocIO" version))
         (sha256
           (base32
-            "0skwnpxl6fkqihidpqrfzzh7b05x11j6jwkiinmhggmv0ggjb5ph"))))
+            "1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr"))))
     (properties `((upstream-name . "BiocIO")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-biocgenerics r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiocIO")
     (synopsis "Standard input and output for Bioconductor packages")
     (description
@@ -13074,21 +13506,18 @@ as well as local access.  Developers can register a file extension, e.g.,
 (define-public r-msmseda
   (package
     (name "r-msmseda")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsEDA" version))
        (sha256
         (base32
-         "0555a3riyp781mlffmnf93igfq8vl8wjk51pa9qb48qkdn6y8pfc"))))
+         "1jammjkjjkcqad2ki02l2pdf4jybyh71hv463aya2ylmzsin5vi9"))))
     (properties `((upstream-name . "msmsEDA")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-gplots" ,r-gplots)
-       ("r-mass" ,r-mass)
-       ("r-msnbase" ,r-msnbase)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+     (list r-gplots r-mass r-msnbase r-rcolorbrewer))
     (home-page
      "https://bioconductor.org/packages/msmsEDA")
     (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
@@ -13100,21 +13529,18 @@ experiments, and visualize de influence of the involved factors.")
 (define-public r-msmstests
   (package
     (name "r-msmstests")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsTests" version))
        (sha256
         (base32
-         "11vhy1l6za73dpdj85q4ksaghgd8vb2h8v9iirmsn2vpajqrvgjh"))))
+         "0xmjgd8rqpb8i7d46pvnj7da2di8bwfdncr48b8hgylkc98ghznb"))))
     (properties `((upstream-name . "msmsTests")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-edger" ,r-edger)
-       ("r-msmseda" ,r-msmseda)
-       ("r-msnbase" ,r-msnbase)
-       ("r-qvalue" ,r-qvalue)))
+     (list r-edger r-msmseda r-msnbase r-qvalue))
     (home-page
      "https://bioconductor.org/packages/msmsTests")
     (synopsis "Differential LC-MS/MS expression tests")
@@ -13132,45 +13558,45 @@ relevant, and the minimum expression of the most abundant condition.")
 (define-public r-catalyst
   (package
     (name "r-catalyst")
-    (version "1.16.2")
+    (version "1.18.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "CATALYST" version))
         (sha256
           (base32
-            "1vw8x54hwgcyn29k81zcvawawy2iy2qgp49gjpb830q04gx6yc6h"))))
+            "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi"))))
     (properties `((upstream-name . "CATALYST")))
     (build-system r-build-system)
     (propagated-inputs
-      `(("r-circlize" ,r-circlize)
-        ("r-complexheatmap" ,r-complexheatmap)
-        ("r-consensusclusterplus" ,r-consensusclusterplus)
-        ("r-cowplot" ,r-cowplot)
-        ("r-data-table" ,r-data-table)
-        ("r-dplyr" ,r-dplyr)
-        ("r-drc" ,r-drc)
-        ("r-flowcore" ,r-flowcore)
-        ("r-flowsom" ,r-flowsom)
-        ("r-ggplot2" ,r-ggplot2)
-        ("r-ggrepel" ,r-ggrepel)
-        ("r-ggridges" ,r-ggridges)
-        ("r-gridextra" ,r-gridextra)
-        ("r-magrittr" ,r-magrittr)
-        ("r-matrix" ,r-matrix)
-        ("r-matrixstats" ,r-matrixstats)
-        ("r-nnls" ,r-nnls)
-        ("r-purrr" ,r-purrr)
-        ("r-rcolorbrewer" ,r-rcolorbrewer)
-        ("r-reshape2" ,r-reshape2)
-        ("r-rtsne" ,r-rtsne)
-        ("r-s4vectors" ,r-s4vectors)
-        ("r-scales" ,r-scales)
-        ("r-scater" ,r-scater)
-        ("r-singlecellexperiment" ,r-singlecellexperiment)
-        ("r-summarizedexperiment" ,r-summarizedexperiment)))
+      (list r-circlize
+            r-complexheatmap
+            r-consensusclusterplus
+            r-cowplot
+            r-data-table
+            r-dplyr
+            r-drc
+            r-flowcore
+            r-flowsom
+            r-ggplot2
+            r-ggrepel
+            r-ggridges
+            r-gridextra
+            r-magrittr
+            r-matrix
+            r-matrixstats
+            r-nnls
+            r-purrr
+            r-rcolorbrewer
+            r-reshape2
+            r-rtsne
+            r-s4vectors
+            r-scales
+            r-scater
+            r-singlecellexperiment
+            r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page
       "https://github.com/HelenaLC/CATALYST")
     (synopsis "Cytometry data analysis tools")
@@ -13190,32 +13616,32 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
 (define-public r-erma
   (package
     (name "r-erma")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "erma" version))
        (sha256
         (base32
-         "02a9702sasgighwb0f9ii8n30ngfx1hjnppaay1f5zsigr8vqalz"))))
+         "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-homo-sapiens" ,r-homo-sapiens)
-       ("r-iranges" ,r-iranges)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-genomeinfodb
+           r-genomicfiles
+           r-genomicranges
+           r-ggplot2
+           r-homo-sapiens
+           r-iranges
+           r-rtracklayer
+           r-s4vectors
+           r-shiny
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/erma")
     (synopsis "Epigenomic road map adventures")
     (description
@@ -13230,14 +13656,14 @@ by Ernst and Kellis.")
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "0k3dxacrwgyrkvm7ggc2s1s1pbfs6c0a7ngykkj7jnc73czvnilx"))))
+         "1svmjaa3gisi39sl52337drvd54havcy5pjmwrykgykz5flid2m7"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -13250,35 +13676,35 @@ by Ernst and Kellis.")
                (("fechable") "fetchable"))
              #t)))))
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationfilter" ,r-annotationfilter)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggally" ,r-ggally)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-gtable" ,r-gtable)
-       ("r-hmisc" ,r-hmisc)
-       ("r-iranges" ,r-iranges)
-       ("r-organismdbi" ,r-organismdbi)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rlang" ,r-rlang)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-annotationdbi
+           r-annotationfilter
+           r-biobase
+           r-biocgenerics
+           r-biostrings
+           r-biovizbase
+           r-bsgenome
+           r-ensembldb
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-ggally
+           r-ggplot2
+           r-gridextra
+           r-gtable
+           r-hmisc
+           r-iranges
+           r-organismdbi
+           r-reshape2
+           r-rlang
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-scales
+           r-summarizedexperiment
+           r-variantannotation))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "http://www.tengfei.name/ggbio/")
     (synopsis "Visualization tools for genomic data")
     (description
@@ -13316,21 +13742,21 @@ interval to data view, mismatch pileup, and several splicing summaries.")
                (("importFrom\\(ff,.*") "import(ff)\n"))
              #t)))))
     (propagated-inputs
-     `(("r-batchjobs" ,r-batchjobs)
-       ("r-bbmisc" ,r-bbmisc)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-bit" ,r-bit)
-       ("r-doparallel" ,r-doparallel)
-       ("r-ff" ,r-ff)
-       ("r-ffbase" ,r-ffbase)
-       ("r-foreach" ,r-foreach)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-batchjobs
+           r-bbmisc
+           r-biocgenerics
+           r-bit
+           r-doparallel
+           r-ff
+           r-ffbase
+           r-foreach
+           r-genomicfiles
+           r-genomicranges
+           r-rtracklayer
+           r-s4vectors
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/gQTLBase")
     (synopsis "Infrastructure for eQTL, mQTL and similar studies")
     (description
@@ -13353,38 +13779,38 @@ and more.")
     (properties `((upstream-name . "gQTLstats")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-batchjobs" ,r-batchjobs)
-       ("r-bbmisc" ,r-bbmisc)
-       ("r-beeswarm" ,r-beeswarm)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dplyr" ,r-dplyr)
-       ("r-erma" ,r-erma)
-       ("r-ffbase" ,r-ffbase)
-       ("r-foreach" ,r-foreach)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggbeeswarm" ,r-ggbeeswarm)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gqtlbase" ,r-gqtlbase)
-       ("r-hardyweinberg" ,r-hardyweinberg)
-       ("r-homo-sapiens" ,r-homo-sapiens)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-mgcv" ,r-mgcv)
-       ("r-plotly" ,r-plotly)
-       ("r-reshape2" ,r-reshape2)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-snpstats" ,r-snpstats)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-annotationdbi
+           r-batchjobs
+           r-bbmisc
+           r-beeswarm
+           r-biobase
+           r-biocgenerics
+           r-doparallel
+           r-dplyr
+           r-erma
+           r-ffbase
+           r-foreach
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicfiles
+           r-genomicranges
+           r-ggbeeswarm
+           r-ggplot2
+           r-gqtlbase
+           r-hardyweinberg
+           r-homo-sapiens
+           r-iranges
+           r-limma
+           r-mgcv
+           r-plotly
+           r-reshape2
+           r-s4vectors
+           r-shiny
+           r-snpstats
+           r-summarizedexperiment
+           r-variantannotation))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/gQTLstats")
     (synopsis "Computationally efficient analysis for eQTL and allied studies")
     (description
@@ -13398,41 +13824,41 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.36.2")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "0lp0k8jd4dfsfn10706124graaqnzcyv1siblvm8dn2ykw2rc6vl"))))
+         "0nqa7m300d7gpsayb6c6rv64d3y8c390wvwgz7v29zs9c025s9a8"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-digest" ,r-digest)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-latticeextra" ,r-latticeextra)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
+     (list r-annotationdbi
+           r-biobase
+           r-biocgenerics
+           r-biomart
+           r-biostrings
+           r-biovizbase
+           r-bsgenome
+           r-digest
+           r-ensembldb
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-lattice
+           r-latticeextra
+           r-matrixstats
+           r-rcolorbrewer
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-xvector))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/Gviz")
     (synopsis "Plotting data and annotation information along genomic coordinates")
     (description
@@ -13447,30 +13873,30 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.24.0")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "0109cxsviq1sk5hfwkjzd0y1kpm934287asjjd0j8jhh4b0ah2b2"))))
+         "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationhub" ,r-annotationhub)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-readr" ,r-readr)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-snpstats" ,r-snpstats)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-annotationdbi
+           r-annotationhub
+           r-biocfilecache
+           r-biostrings
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-readr
+           r-s4vectors
+           r-snpstats
+           r-variantannotation))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/gwascat")
     (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
     (description
@@ -13481,20 +13907,17 @@ EMBL-EBI GWAS catalog.")
 (define-public r-kegggraph
   (package
     (name "r-kegggraph")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGgraph" version))
        (sha256
-        (base32 "0zxdph5hzr3kzj2g1mjqpiviwa189a5sq4bw7wiry6r79fdnklqs"))))
+        (base32 "1qqvbv1sq9j570syb2802ya2ffg1k8f1w986wr6ksqkwxb9qbbm4"))))
     (properties `((upstream-name . "KEGGgraph")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-graph" ,r-graph)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rgraphviz" ,r-rgraphviz)
-       ("r-xml" ,r-xml)))
+     (list r-graph r-rcurl r-rgraphviz r-xml))
     (home-page "https://bioconductor.org/packages/KEGGgraph")
     (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
     (description
@@ -13508,28 +13931,28 @@ functionalities including parsing, graph operation, visualization and etc.")
 (define-public r-ldblock
   (package
     (name "r-ldblock")
-    (version "1.22.1")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ldblock" version))
        (sha256
         (base32
-         "16vp5psmigxdkkd6fbivb6s8mvd7rsnm771wsbjvayl2y7ig7kq4"))))
+         "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-httr" ,r-httr)
-       ("r-matrix" ,r-matrix)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-snpstats" ,r-snpstats)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-biocgenerics
+           r-ensdb-hsapiens-v75
+           r-ensembldb
+           r-genomeinfodb
+           r-genomicfiles
+           r-httr
+           r-matrix
+           r-rsamtools
+           r-snpstats
+           r-variantannotation))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/ldblock")
     (synopsis "Data structures for linkage disequilibrium measures in populations")
     (description
@@ -13555,9 +13978,7 @@ defining LD blocks.")
     (properties `((upstream-name . "LDheatmap")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-genetics" ,r-genetics)
-       ("r-rcpp" ,r-rcpp)
-       ("r-snpstats" ,r-snpstats)))
+     (list r-genetics r-rcpp r-snpstats))
     (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
     (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
     (description
@@ -13572,24 +13993,26 @@ on the plot.")
 (define-public r-abn
   (package
     (name "r-abn")
-    (version "2.5-0")
+    (version "2.6-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abn" version))
        (sha256
         (base32
-         "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw"))))
+         "0fr5pyc43hly5ry5bbygibbh9mnql7vl4r5qz42d0ry4hahyxa4w"))))
     (build-system r-build-system)
     (inputs
-     `(("gsl" ,gsl)))
+     (list gsl))
     (propagated-inputs
-     `(("r-lme4" ,r-lme4)
-       ("r-nnet" ,r-nnet)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-rgraphviz" ,r-rgraphviz)
-       ("r-rjags" ,r-rjags)))
+     (list r-doparallel
+           r-foreach
+           r-lme4
+           r-nnet
+           r-rcpp
+           r-rcpparmadillo
+           r-rgraphviz
+           r-rjags))
     (home-page "https://r-bayesian-networks.org/")
     (synopsis "Modelling multivariate data with additive bayesian networks")
     (description
@@ -13619,12 +14042,9 @@ statistical dependencies in messy, complex data.")
                 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
     (build-system r-build-system)
     (inputs
-     `(("zlib" ,zlib)))
+     (list zlib))
     (propagated-inputs
-     `(("r-bh" ,r-bh)
-       ("r-catools" ,r-catools)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rsamtools" ,r-rsamtools)))
+     (list r-bh r-catools r-rcpp r-rsamtools))
     (home-page "https://cran.r-project.org/web/packages/spp/")
     (synopsis "ChIP-Seq processing pipeline")
     (description "This package provides tools for analysis of ChIP-seq and
@@ -13634,24 +14054,24 @@ other functional sequencing data.")
 (define-public r-pathview
   (package
     (name "r-pathview")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pathview" version))
        (sha256
-        (base32 "1fank0qavv9ikmzxvms8mky2wbzny02rfqkvsqzma26r3vl4r1g1"))))
+        (base32 "1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr"))))
     (properties `((upstream-name . "pathview")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-graph" ,r-graph)
-       ("r-kegggraph" ,r-kegggraph)
-       ("r-keggrest" ,r-keggrest)
-       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
-       ("r-png" ,r-png)
-       ("r-rgraphviz" ,r-rgraphviz)
-       ("r-xml" ,r-xml)))
+     (list r-annotationdbi
+           r-graph
+           r-kegggraph
+           r-keggrest
+           r-org-hs-eg-db
+           r-png
+           r-rgraphviz
+           r-xml))
     (home-page "https://pathview.uncc.edu/")
     (synopsis "Tool set for pathway based data integration and visualization")
     (description
@@ -13668,22 +14088,19 @@ large-scale and fully automated analysis.")
 (define-public r-snpstats
   (package
     (name "r-snpstats")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "snpStats" version))
        (sha256
         (base32
-         "11vvih5y9kvyjfp2navkfpp4xiyfgwlv4r0x3p52hkj92pc2pg3g"))))
+         "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq"))))
     (properties `((upstream-name . "snpStats")))
     (build-system r-build-system)
-    (inputs `(("zlib" ,zlib)))
+    (inputs (list zlib))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-matrix" ,r-matrix)
-       ("r-survival" ,r-survival)
-       ("r-zlibbioc" ,r-zlibbioc)))
+     (list r-biocgenerics r-matrix r-survival r-zlibbioc))
     (home-page "https://bioconductor.org/packages/snpStats")
     (synopsis "Methods for SNP association studies")
     (description
@@ -13695,32 +14112,32 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
 (define-public r-chromstar
   (package
     (name "r-chromstar")
-    (version "1.18.0")
+    (version "1.20.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromstaR" version))
        (sha256
         (base32
-         "09cqzylci4x4i7wn4ckcqhdlljbzfrp08wdvkkc5vrdldnj9pq5h"))))
+         "1akcmxzn4j9ph4n3lsgfh8fh8hrb28jjamz037w59bsdkcv6wyjq"))))
     (properties `((upstream-name . "chromstaR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bamsignals" ,r-bamsignals)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-chromstardata" ,r-chromstardata)
-       ("r-doparallel" ,r-doparallel)
-       ("r-foreach" ,r-foreach)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-mvtnorm" ,r-mvtnorm)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-bamsignals
+           r-biocgenerics
+           r-chromstardata
+           r-doparallel
+           r-foreach
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-mvtnorm
+           r-reshape2
+           r-rsamtools
+           r-s4vectors))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/ataudt/chromstaR")
     (synopsis "Chromatin state analysis for ChIP-Seq data")
     (description
@@ -13733,27 +14150,27 @@ analyses.")
 (define-public r-guitar
   (package
     (name "r-guitar")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Guitar" version))
        (sha256
         (base32
-         "1q4m6c5181dw12lvdp324jlk78c9jgcsg6b9hk87zjadp6j0gfr6"))))
+         "082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9"))))
     (properties `((upstream-name . "Guitar")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-knitr" ,r-knitr)
-       ("r-magrittr" ,r-magrittr)
-       ("r-rtracklayer" ,r-rtracklayer)))
+     (list r-annotationdbi
+           r-dplyr
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-knitr
+           r-magrittr
+           r-rtracklayer))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/Guitar")
     (synopsis "Visualize genomic features")
     (description
@@ -13765,18 +14182,17 @@ starting site, start codon, stop codon and transcription ending site.")
 (define-public r-sushi
   (package
     (name "r-sushi")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Sushi" version))
               (sha256
                (base32
-                "1m5l0nflhcynb3gz7b8qzvknb0s6xhds8z1yl3mbv8ic9qn2knv4"))))
+                "073mh1d063ph5zk1d8kipgblr4l1ixqbxflhq4669761fi2frlw4"))))
     (properties `((upstream-name . "Sushi")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biomart" ,r-biomart)
-       ("r-zoo" ,r-zoo)))
+     (list r-biomart r-zoo))
     (home-page "https://bioconductor.org/packages/Sushi")
     (synopsis "Tools for visualizing genomics data")
     (description
@@ -13787,28 +14203,28 @@ visualizations for publication-quality multi-panel figures.")
 (define-public r-ballgown
   (package
     (name "r-ballgown")
-    (version "2.24.0")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ballgown" version))
        (sha256
         (base32
-         "0ff8z4pfgzai2q4aafclg36bhsi9jwl9xhh1p9fqhmikisscq7i1"))))
+         "0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf"))))
     (properties `((upstream-name . "ballgown")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-sva" ,r-sva)))
+     (list r-biobase
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-limma
+           r-rcolorbrewer
+           r-rtracklayer
+           r-s4vectors
+           r-sva))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/ballgown")
     (synopsis "Flexible, isoform-level differential expression analysis")
     (description
@@ -13821,27 +14237,27 @@ to annotation.")
 (define-public r-megadepth
   (package
     (name "r-megadepth")
-    (version "1.2.3")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "megadepth" version))
        (sha256
         (base32
-         "0grgj7bzyqnxby0sx5ic1h9bzmx19xwl0a5b3v6wbnwqcla2i3kg"))))
+         "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r"))))
     (properties `((upstream-name . "megadepth")))
     (build-system r-build-system)
-    (inputs `(("megadepth" ,megadepth)))
+    (inputs (list megadepth))
     (propagated-inputs
-     `(("r-cmdfun" ,r-cmdfun)
-       ("r-dplyr" ,r-dplyr)
-       ("r-fs" ,r-fs)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-magrittr" ,r-magrittr)
-       ("r-readr" ,r-readr)
-       ("r-xfun" ,r-xfun)))
+     (list r-cmdfun
+           r-dplyr
+           r-fs
+           r-genomicranges
+           r-magrittr
+           r-readr
+           r-xfun))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/LieberInstitute/megadepth")
     (synopsis "BigWig and BAM related utilities")
     (description
@@ -13854,27 +14270,27 @@ regions or annotations of your choice from BigWig files.")
 (define-public r-beclear
   (package
     (name "r-beclear")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BEclear" version))
        (sha256
         (base32
-         "0w18livng2gcmjgvws7pix3gsnj237rs34sgwxsfmn8p5vfx8b30"))))
+         "1njb1lfd4wmsrfw06jc8z8vdk14nmcw9lwyvbxr7z1zg4h8v6c29"))))
     (properties `((upstream-name . "BEclear")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-abind" ,r-abind)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-data-table" ,r-data-table)
-       ("r-futile-logger" ,r-futile-logger)
-       ("r-matrix" ,r-matrix)
-       ("r-outliers" ,r-outliers)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rdpack" ,r-rdpack)))
+     (list r-abind
+           r-biocparallel
+           r-data-table
+           r-futile-logger
+           r-matrix
+           r-outliers
+           r-rcpp
+           r-rdpack))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/uds-helms/BEclear")
     (synopsis "Correction of batch effects in DNA methylation data")
     (description
@@ -13887,34 +14303,34 @@ real numbers.")
 (define-public r-bgeecall
   (package
     (name "r-bgeecall")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeCall" version))
        (sha256
         (base32
-         "1byciy7vzbdkdgaim10s9qb7zlxsywbhcsrka31gm0rm9ljqc665"))))
+         "0rbbl8m48qcvl26lnf27jq108p7pi84m9ac3qcpjc0ax5wywbv16"))))
     (properties `((upstream-name . "BgeeCall")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("kallisto" ,kallisto)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-data-table" ,r-data-table)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-rhdf5" ,r-rhdf5)
-       ("r-rslurm" ,r-rslurm)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-sjmisc" ,r-sjmisc)
-       ("r-tximport" ,r-tximport)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list kallisto
+           r-biomart
+           r-biostrings
+           r-data-table
+           r-dplyr
+           r-genomicfeatures
+           r-jsonlite
+           r-rhdf5
+           r-rslurm
+           r-rtracklayer
+           r-sjmisc
+           r-tximport))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/BgeeDB/BgeeCall")
     (synopsis "RNA-Seq present/absent gene expression calls generation")
     (description
-     "BgeeCall allows to generate present/absent gene expression calls without
+     "BgeeCall allows generating present/absent gene expression calls without
 using an arbitrary cutoff like TPM<1.  Calls are generated based on reference
 intergenic sequences.  These sequences are generated based on expression of
 all RNA-Seq libraries of each species integrated in Bgee.")
@@ -13923,29 +14339,29 @@ all RNA-Seq libraries of each species integrated in Bgee.")
 (define-public r-bgeedb
   (package
     (name "r-bgeedb")
-    (version "2.18.1")
+    (version "2.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeDB" version))
        (sha256
         (base32
-         "1ziq180yfpdqwhjdzkwjjhwzn3kb0gkj6q0a26c7a30mcfb50w11"))))
+         "0pjymal01sjl5dc37g66wykgxnksarlbvwnbvhg7w0i7y92zavqk"))))
     (properties `((upstream-name . "BgeeDB")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-curl" ,r-curl)
-       ("r-data-table" ,r-data-table)
-       ("r-digest" ,r-digest)
-       ("r-dplyr" ,r-dplyr)
-       ("r-graph" ,r-graph)
-       ("r-r-utils" ,r-r-utils)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-tidyr" ,r-tidyr)
-       ("r-topgo" ,r-topgo)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-biobase
+           r-curl
+           r-data-table
+           r-digest
+           r-dplyr
+           r-graph
+           r-r-utils
+           r-rcurl
+           r-rsqlite
+           r-tidyr
+           r-topgo))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/BgeeDB/BgeeDB_R")
     (synopsis "Annotation and gene expression data retrieval from Bgee database")
     (description
@@ -13957,22 +14373,19 @@ anatomical terms, mapped to genes by expression patterns.")
 (define-public r-biobtreer
   (package
     (name "r-biobtreer")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobtreeR" version))
        (sha256
         (base32
-         "0pynx4ps1qxsn13ba6zyg6h5dqlp2y7qish67m7sdjns079zh061"))))
+         "0m9gx2g5ishbbh7aqp09mpknhr7q1v5ap0s6xp6ccj01pz2gkk8s"))))
     (properties `((upstream-name . "biobtreeR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-httpuv" ,r-httpuv)
-       ("r-httr" ,r-httr)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-stringi" ,r-stringi)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-httpuv r-httr r-jsonlite r-stringi))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/tamerh/biobtreeR")
     (synopsis "Use biobtree tool from R")
     (description
@@ -13984,18 +14397,18 @@ mappings functionalities.")
 (define-public r-minet
   (package
     (name "r-minet")
-    (version "3.50.0")
+    (version "3.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minet" version))
        (sha256
         (base32
-         "0bir2zr4r2wawkdvdhrk2hcyxmgkrkfvx36jj85fcm24axlqrzzb"))))
+         "0nhgvgci4r9pjfsnvxyj2q8im1wvig4zmfx2kidw8f63x2ip2rbd"))))
     (properties `((upstream-name . "minet")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-infotheo" ,r-infotheo)))
+     (list r-infotheo))
     (home-page "http://minet.meyerp.com")
     (synopsis "Mutual information networks")
     (description
@@ -14006,22 +14419,19 @@ information networks from data.")
 (define-public r-genetclassifier
   (package
     (name "r-genetclassifier")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geNetClassifier" version))
        (sha256
         (base32
-         "1i1cavbbvxzqgqxfmikghnls18jrq12hb953mjrwa95lkhzdxm2d"))))
+         "1phyphdc1i55ab1a05633b0p41q8n7w0byp1plgcav2s3h8mk1km"))))
     (properties
      `((upstream-name . "geNetClassifier")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-e1071" ,r-e1071)
-       ("r-ebarrays" ,r-ebarrays)
-       ("r-minet" ,r-minet)))
+     (list r-biobase r-e1071 r-ebarrays r-minet))
     (home-page "https://www.cicancer.org")
     (synopsis "Classify diseases and build gene networks using expression profiles")
     (description
@@ -14034,18 +14444,18 @@ interface to query the classifier.")
 (define-public r-dir-expiry
   (package
     (name "r-dir-expiry")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dir.expiry" version))
        (sha256
         (base32
-         "05mk7iwzay1xrgvssbz7nyl5d1n03syalbk18lmjmbx05dy0cjik"))))
+         "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00"))))
     (properties `((upstream-name . "dir.expiry")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-filelock" ,r-filelock)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+    (propagated-inputs (list r-filelock))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/dir.expiry")
     (synopsis "Managing expiration for cache directories")
     (description
@@ -14058,20 +14468,20 @@ eliminating obsolete caches generated by old versions of packages.")
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "basilisk.utils" version))
        (sha256
         (base32
-         "0qbm6rj6h059hakflbwz4j4f59311jhbk5dnpx11kyixh5pgjk7v"))))
+         "0578rq2yz24sv7anb7vp0a0y35944ag1l8ca6haanb03wl97wm99"))))
     (properties
      `((upstream-name . "basilisk.utils")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-dir-expiry" ,r-dir-expiry)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-dir-expiry))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/basilisk.utils")
     (synopsis "Basilisk installation utilities")
     (description
@@ -14082,21 +14492,19 @@ package, primarily for creation of the underlying Conda instance.")
 (define-public r-basilisk
   (package
     (name "r-basilisk")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "basilisk" version))
        (sha256
         (base32
-         "1nzbn3f2jzvg3a3m6wgksi4cvamqas2q7csdk4ir7fcirasf536v"))))
+         "1cdkpngv9qybd9yxc3i2201p433vkkahs71v28x6lgs5l2wz3m1a"))))
     (properties `((upstream-name . "basilisk")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-basilisk-utils" ,r-basilisk-utils)
-       ("r-dir-expiry" ,r-dir-expiry)
-       ("r-reticulate" ,r-reticulate)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-basilisk-utils r-dir-expiry r-reticulate))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/basilisk")
     (synopsis "Freeze Python dependencies inside Bioconductor packages")
     (description
@@ -14110,24 +14518,29 @@ Python environments in a single R session.")
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocthis" version))
        (sha256
         (base32
-         "08awghsg7q22csb0j9dr8dpb1vkn9gcs9qnhhljxifkw2ahbqia4"))))
+         "0kh5lmv992v4r5r58x29403cll0zxr9fx4ar81nrzvnch5668v39"))))
     (properties `((upstream-name . "biocthis")))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-HOME
+           (lambda _ (setenv "HOME" "/tmp"))))))
     (propagated-inputs
-     `(("r-biocmanager" ,r-biocmanager)
-       ("r-fs" ,r-fs)
-       ("r-glue" ,r-glue)
-       ("r-rlang" ,r-rlang)
-       ("r-styler" ,r-styler)
-       ("r-usethis" ,r-usethis)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-biocmanager
+           r-fs
+           r-glue
+           r-rlang
+           r-styler
+           r-usethis))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/lcolladotor/biocthis")
     (synopsis "Automate package and project setup for Bioconductor packages")
     (description
@@ -14139,25 +14552,25 @@ Bioconductor-friendly.")
 (define-public r-biocdockermanager
   (package
     (name "r-biocdockermanager")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocDockerManager" version))
        (sha256
         (base32
-         "0dh1flm5chsdcihljrg6znjskqkp0qyjh39hsv4zq0frf1rm97j7"))))
+         "1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w"))))
     (properties
      `((upstream-name . "BiocDockerManager")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("docker" ,docker)
-       ("r-dplyr" ,r-dplyr)
-       ("r-httr" ,r-httr)
-       ("r-memoise" ,r-memoise)
-       ("r-readr" ,r-readr)
-       ("r-whisker" ,r-whisker)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list docker
+           r-dplyr
+           r-httr
+           r-memoise
+           r-readr
+           r-whisker))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/BiocDockerManager")
     (synopsis "Access and manage Bioconductor Docker images")
     (description
@@ -14169,35 +14582,36 @@ the Bioconductor project.")
 (define-public r-biodb
   (package
     (name "r-biodb")
-    (version "1.0.4")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biodb" version))
        (sha256
         (base32
-         "1apnbr5p619nsrhd2drm6arj69sw0wijv8ap7dfrndqkffrpbfmx"))))
+         "0b5zva16r4kz8736h3djjgmh35nxmlin4f374rb4i2s55zsrb638"))))
     (properties `((upstream-name . "biodb")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-chk" ,r-chk)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-lgr" ,r-lgr)
-       ("r-lifecycle" ,r-lifecycle)
-       ("r-openssl" ,r-openssl)
-       ("r-plyr" ,r-plyr)
-       ("r-progress" ,r-progress)
-       ("r-r6" ,r-r6)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-stringr" ,r-stringr)
-       ("r-testthat" ,r-testthat)
-       ("r-withr" ,r-withr)
-       ("r-xml" ,r-xml)
-       ("r-yaml" ,r-yaml)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-biocfilecache
+           r-chk
+           r-jsonlite
+           r-lgr
+           r-lifecycle
+           r-openssl
+           r-plyr
+           r-progress
+           r-r6
+           r-rappdirs
+           r-rcpp
+           r-rcurl
+           r-rsqlite
+           r-stringr
+           r-testthat
+           r-withr
+           r-xml
+           r-yaml))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/biodb")
     (synopsis "Library for connecting to chemical and biological databases")
     (description
@@ -14213,22 +14627,19 @@ separate published packages.")
 (define-public r-biomformat
   (package
     (name "r-biomformat")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomformat" version))
        (sha256
         (base32
-         "1wgshkddxbmpsihpkm0dp7vqp59ns6iqbx574y80n2pxb8dx8sy9"))))
+         "0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817"))))
     (properties `((upstream-name . "biomformat")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-jsonlite" ,r-jsonlite)
-       ("r-matrix" ,r-matrix)
-       ("r-plyr" ,r-plyr)
-       ("r-rhdf5" ,r-rhdf5)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-jsonlite r-matrix r-plyr r-rhdf5))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/joey711/biomformat/")
     (synopsis "Interface package for the BIOM file format")
     (description
@@ -14245,14 +14656,14 @@ as extensions of common core functions/methods.")
 (define-public r-mvcclass
   (package
     (name "r-mvcclass")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MVCClass" version))
        (sha256
         (base32
-         "1di7y10mr7caacd6igwxnr62cm4v1x877yi4a2i5jqz1058jqni7"))))
+         "088gzh33vjkjf78xczqfs89pyg0k7c3533yfvijqxl84ni2ky78z"))))
     (properties `((upstream-name . "MVCClass")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/MVCClass")
@@ -14265,21 +14676,18 @@ design.")
 (define-public r-biomvcclass
   (package
     (name "r-biomvcclass")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioMVCClass" version))
        (sha256
         (base32
-         "04pld93nffbci47dnf0awmcmhlfzv599ggcd7hvq78w41ac60qv8"))))
+         "0jqgazwz35gz11a7vzanyy2yalzalx0z0rw6y18nmk8dbv01nv2j"))))
     (properties `((upstream-name . "BioMVCClass")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-graph" ,r-graph)
-       ("r-mvcclass" ,r-mvcclass)
-       ("r-rgraphviz" ,r-rgraphviz)))
+     (list r-biobase r-graph r-mvcclass r-rgraphviz))
     (home-page "https://bioconductor.org/packages/BioMVCClass")
     (synopsis "Model-View-Controller (MVC) classes that use Biobase")
     (description
@@ -14290,21 +14698,18 @@ design.")
 (define-public r-biomvrcns
   (package
     (name "r-biomvrcns")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomvRCNS" version))
        (sha256
         (base32
-         "0wyzj422smr4m9mswzn9inc1sn86pnia7jmd6k28nd2a7fjyrm16"))))
+         "01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy"))))
     (properties `((upstream-name . "biomvRCNS")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-genomicranges" ,r-genomicranges)
-       ("r-gviz" ,r-gviz)
-       ("r-iranges" ,r-iranges)
-       ("r-mvtnorm" ,r-mvtnorm)))
+     (list r-genomicranges r-gviz r-iranges r-mvtnorm))
     (home-page "https://bioconductor.org/packages/biomvRCNS")
     (synopsis "Copy number study and segmentation for multivariate biological data")
     (description
@@ -14318,39 +14723,39 @@ using aCGH or sequencing.")
 (define-public r-bionero
   (package
     (name "r-bionero")
-    (version "1.0.4")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNERO" version))
        (sha256
         (base32
-         "1yj0pavyfrj2gsvaj1dkgmznibm2appxjx9rk5qjslhslmm5b05b"))))
+         "0ddrzv1g46hvm52dzrcj5nbyyw9a16cqk8zg20wnkrh3qw1h4d9p"))))
     (properties `((upstream-name . "BioNERO")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-complexheatmap" ,r-complexheatmap)
-       ("r-deseq2" ,r-deseq2)
-       ("r-dynamictreecut" ,r-dynamictreecut)
-       ("r-genie3" ,r-genie3)
-       ("r-ggnetwork" ,r-ggnetwork)
-       ("r-ggnewscale" ,r-ggnewscale)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggpubr" ,r-ggpubr)
-       ("r-igraph" ,r-igraph)
-       ("r-intergraph" ,r-intergraph)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-minet" ,r-minet)
-       ("r-netrep" ,r-netrep)
-       ("r-networkd3" ,r-networkd3)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-reshape2" ,r-reshape2)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-sva" ,r-sva)
-       ("r-wgcna" ,r-wgcna)))
+     (list r-biocparallel
+           r-complexheatmap
+           r-deseq2
+           r-dynamictreecut
+           r-genie3
+           r-ggnetwork
+           r-ggnewscale
+           r-ggplot2
+           r-ggpubr
+           r-igraph
+           r-intergraph
+           r-matrixstats
+           r-minet
+           r-netrep
+           r-networkd3
+           r-rcolorbrewer
+           r-reshape2
+           r-summarizedexperiment
+           r-sva
+           r-wgcna))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/almeidasilvaf/BioNERO")
     (synopsis "Biological network reconstruction omnibus")
     (description
@@ -14374,22 +14779,18 @@ networks.")
 (define-public r-bionet
   (package
     (name "r-bionet")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNet" version))
        (sha256
         (base32
-         "15rk1jfv4h1mxvr5bs0qmq6fdnza7zcmksigqxb46fs7f6znr3yi"))))
+         "05rj14jn4gn0hfn57amf19b8fqwkd3y2ji3mg7m1yg1w7n4qxqsg"))))
     (properties `((upstream-name . "BioNet")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-graph" ,r-graph)
-       ("r-igraph" ,r-igraph)
-       ("r-rbgl" ,r-rbgl)))
+     (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
     (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
     (synopsis "Functional analysis of biological networks")
     (description
@@ -14407,37 +14808,37 @@ scoring subnetwork.")
 (define-public r-bionetstat
   (package
     (name "r-bionetstat")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNetStat" version))
        (sha256
         (base32
-         "16xlfng9m8xvm831c2x6zmjc0gavlfiy9pnza55hdv86888fcnbg"))))
+         "13br8x4809hrr4ibz6iy5qjza9j6cazmkpvfikvw6bs588csxwf8"))))
     (properties `((upstream-name . "BioNetStat")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-dt" ,r-dt)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-hmisc" ,r-hmisc)
-       ("r-igraph" ,r-igraph)
-       ("r-knitr" ,r-knitr)
-       ("r-markdown" ,r-markdown)
-       ("r-pathview" ,r-pathview)
-       ("r-pheatmap" ,r-pheatmap)
-       ("r-plyr" ,r-plyr)
-       ("r-psych" ,r-psych)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rjsonio" ,r-rjsonio)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("r-shiny" ,r-shiny)
-       ("r-shinybs" ,r-shinybs)
-       ("r-whisker" ,r-whisker)
-       ("r-yaml" ,r-yaml)))
+     (list r-biocparallel
+           r-dt
+           r-ggplot2
+           r-hmisc
+           r-igraph
+           r-knitr
+           r-markdown
+           r-pathview
+           r-pheatmap
+           r-plyr
+           r-psych
+           r-rcolorbrewer
+           r-rjsonio
+           r-rmarkdown
+           r-shiny
+           r-shinybs
+           r-whisker
+           r-yaml))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/jardimViniciusC/BioNetStat")
     (synopsis "Biological network analysis")
     (description
@@ -14449,22 +14850,20 @@ network and metabolic pathways view.")
 (define-public r-bioqc
   (package
     (name "r-bioqc")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioQC" version))
        (sha256
         (base32
-         "04akp94p0d0zid55m1b1k3qlw7iq914pcg57lihgj3pa92n1sc5l"))))
+         "190336qk0plg79gzvfn6wfplsi8nq0nj8508g7m0w3z6bdgwy407"))))
     (properties `((upstream-name . "BioQC")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-edger" ,r-edger)
-       ("r-rcpp" ,r-rcpp)))
+     (list r-biobase r-edger r-rcpp))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://accio.github.io/BioQC/")
     (synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
     (description
@@ -14477,26 +14876,26 @@ optimised for high performance.")
 (define-public r-biotip
   (package
     (name "r-biotip")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioTIP" version))
        (sha256
         (base32
-         "1i6r8px0fmdjx8frpljppwql74mhx08ibvhs9y3qk91ck5h3f0js"))))
+         "0xmy5c4i9gf6d04gara6lbnnldqmzjaascb2pd2ih60jw2mvl4ys"))))
     (properties `((upstream-name . "BioTIP")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-cluster" ,r-cluster)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-hmisc" ,r-hmisc)
-       ("r-igraph" ,r-igraph)
-       ("r-mass" ,r-mass)
-       ("r-psych" ,r-psych)
-       ("r-stringr" ,r-stringr)))
+     (list r-cluster
+           r-genomicranges
+           r-hmisc
+           r-igraph
+           r-mass
+           r-psych
+           r-stringr))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/xyang2uchicago/BioTIP")
     (synopsis "R package for characterization of biological tipping-point")
     (description
@@ -14507,33 +14906,31 @@ help unravel disease regulatory trajectory.")
 (define-public r-biotmle
   (package
     (name "r-biotmle")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biotmle" version))
        (sha256
         (base32
-         "01smkmbv40yprgrgi2gjnmi8ncqyrlkfdxsh33ki20amcx32nc7f"))))
+         "0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g"))))
     (properties `((upstream-name . "biotmle")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-assertthat" ,r-assertthat)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-dofuture" ,r-dofuture)
-       ("r-dplyr" ,r-dplyr)
-       ("r-drtmle" ,r-drtmle)
-       ("r-future" ,r-future)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggsci" ,r-ggsci)
-       ("r-limma" ,r-limma)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-superheat" ,r-superheat)
-       ("r-tibble" ,r-tibble)))
+     (list r-assertthat
+           r-biocgenerics
+           r-biocparallel
+           r-dplyr
+           r-drtmle
+           r-ggplot2
+           r-ggsci
+           r-limma
+           r-s4vectors
+           r-summarizedexperiment
+           r-superheat
+           r-tibble))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://code.nimahejazi.org/biotmle/")
     (synopsis "Targeted learning with moderated statistics for biomarker discovery")
     (description
@@ -14551,42 +14948,42 @@ ensemble machine learning for the estimation of nuisance functions.")
 (define-public r-bsseq
   (package
     (name "r-bsseq")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bsseq" version))
        (sha256
         (base32
-         "1xpv85hr681kkkilsnasndkszwmzbzq11y0lff4na2ilsm7sqmmi"))))
+         "1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d"))))
     (properties `((upstream-name . "bsseq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-data-table" ,r-data-table)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gtools" ,r-gtools)
-       ("r-hdf5array" ,r-hdf5array)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-locfit" ,r-locfit)
-       ("r-permute" ,r-permute)
-       ("r-r-utils" ,r-r-utils)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhdf5" ,r-rhdf5)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+     (list r-beachmat
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-biostrings
+           r-bsgenome
+           r-data-table
+           r-delayedarray
+           r-delayedmatrixstats
+           r-genomeinfodb
+           r-genomicranges
+           r-gtools
+           r-hdf5array
+           r-iranges
+           r-limma
+           r-locfit
+           r-permute
+           r-r-utils
+           r-rcpp
+           r-rhdf5
+           r-s4vectors
+           r-scales
+           r-summarizedexperiment))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/hansenlab/bsseq")
     (synopsis "Analyze, manage and store bisulfite sequencing data")
     (description
@@ -14597,36 +14994,36 @@ visualizing bisulfite sequencing data.")
 (define-public r-dmrseq
   (package
     (name "r-dmrseq")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dmrseq" version))
        (sha256
         (base32
-         "1jbbjifjsnk9261wqmdwkbzj1w52g6vaanpk4w816ri0fap587m4"))))
+         "1d6y6rbvcgprmzqkdzxg5csf0yv845d9vw10pcd1pzyndrama1vd"))))
     (properties `((upstream-name . "dmrseq")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationhub" ,r-annotationhub)
-       ("r-annotatr" ,r-annotatr)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-bsseq" ,r-bsseq)
-       ("r-bumphunter" ,r-bumphunter)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-locfit" ,r-locfit)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-nlme" ,r-nlme)
-       ("r-outliers" ,r-outliers)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+     (list r-annotationhub
+           r-annotatr
+           r-biocparallel
+           r-bsseq
+           r-bumphunter
+           r-delayedmatrixstats
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-locfit
+           r-matrixstats
+           r-nlme
+           r-outliers
+           r-rcolorbrewer
+           r-rtracklayer
+           r-s4vectors))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/dmrseq")
     (synopsis "Detection and inference of differentially methylated regions")
     (description
@@ -14643,13 +15040,13 @@ interest on transformed methylation proportions.")
 (define-public r-omnipathr
   (package
     (name "r-omnipathr")
-    (version "3.0.4")
+    (version "3.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OmnipathR" version))
        (sha256
-        (base32 "0rbq3h3cp5dgpy5ifmbnfm6z8w4jv45wjzyl1f4qacgrbyf2l30a"))))
+        (base32 "1q89mxnp8cig9r1499g7fb9p9x9ryz1dmc3w6ps5ww9n6rl8jqk8"))))
     (properties `((upstream-name . "OmnipathR")))
     (build-system r-build-system)
     (arguments
@@ -14658,29 +15055,30 @@ interest on transformed methylation proportions.")
          (add-after 'unpack 'set-HOME
            (lambda _ (setenv "HOME" "/tmp"))))))
     (propagated-inputs
-     `(("r-checkmate" ,r-checkmate)
-       ("r-curl" ,r-curl)
-       ("r-digest" ,r-digest)
-       ("r-dplyr" ,r-dplyr)
-       ("r-httr" ,r-httr)
-       ("r-igraph" ,r-igraph)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-later" ,r-later)
-       ("r-logger" ,r-logger)
-       ("r-magrittr" ,r-magrittr)
-       ("r-progress" ,r-progress)
-       ("r-purrr" ,r-purrr)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-readr" ,r-readr)
-       ("r-readxl" ,r-readxl)
-       ("r-rlang" ,r-rlang)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)
-       ("r-tidyselect" ,r-tidyselect)
-       ("r-xml2" ,r-xml2)
-       ("r-yaml" ,r-yaml)))
-    (native-inputs `(("r-knitr" ,r-knitr)))
+     (list r-checkmate
+           r-crayon
+           r-curl
+           r-digest
+           r-dplyr
+           r-httr
+           r-igraph
+           r-jsonlite
+           r-later
+           r-logger
+           r-magrittr
+           r-progress
+           r-purrr
+           r-rappdirs
+           r-readr
+           r-readxl
+           r-rlang
+           r-stringr
+           r-tibble
+           r-tidyr
+           r-tidyselect
+           r-xml2
+           r-yaml))
+    (native-inputs (list r-knitr))
     (home-page "https://saezlab.github.io/OmnipathR/")
     (synopsis "OmniPath web service client and more")
     (description
@@ -14694,45 +15092,45 @@ for ligand activity prediction from transcriptomics data.")
 (define-public r-biscuiteer
   (package
     (name "r-biscuiteer")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biscuiteer" version))
        (sha256
         (base32
-         "0f4kk4v2c5diq0fbvyvgwjd1kjk9izr6n9wfrlrr7wbx4pz3c3h6"))))
+         "16ds322b21g8ys5c3lkrvi70i82f9rxvnknbiqx4sp6f2l01j5yj"))))
     (properties `((upstream-name . "biscuiteer")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biscuiteerdata" ,r-biscuiteerdata)
-       ("r-bsseq" ,r-bsseq)
-       ("r-data-table" ,r-data-table)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-dmrseq" ,r-dmrseq)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gtools" ,r-gtools)
-       ("r-hdf5array" ,r-hdf5array)
-       ("r-homo-sapiens" ,r-homo-sapiens)
-       ("r-impute" ,r-impute)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-mus-musculus" ,r-mus-musculus)
-       ("r-qdnaseq" ,r-qdnaseq)
-       ("r-qualv" ,r-qualv)
-       ("r-r-utils" ,r-r-utils)
-       ("r-readr" ,r-readr)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
+     (list r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-biscuiteerdata
+           r-bsseq
+           r-data-table
+           r-delayedmatrixstats
+           r-dmrseq
+           r-genomeinfodb
+           r-genomicranges
+           r-gtools
+           r-hdf5array
+           r-homo-sapiens
+           r-impute
+           r-matrix
+           r-matrixstats
+           r-mus-musculus
+           r-qdnaseq
+           r-qualv
+           r-r-utils
+           r-readr
+           r-rsamtools
+           r-rtracklayer
+           r-s4vectors
+           r-summarizedexperiment
+           r-variantannotation))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/trichelab/biscuiteer")
     (synopsis "Convenience functions for the Biscuit package")
     (description
@@ -14742,37 +15140,92 @@ samples, with or without imputation, dropping of mostly-NA rows, age
 estimates, etc.")
     (license license:gpl3)))
 
+(define-public r-tcgabiolinks
+  (package
+    (name "r-tcgabiolinks")
+    (version "2.22.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "TCGAbiolinks" version))
+       (sha256
+        (base32 "0l7hfwgd8aiqv2k98jchkr3sdp9hwdg7pzm3bnvr6k7p93ifr6wc"))))
+    (properties `((upstream-name . "TCGAbiolinks")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biomart
+           r-data-table
+           r-downloader
+           r-dplyr
+           r-genomicranges
+           r-ggplot2
+           r-httr
+           r-iranges
+           r-jsonlite
+           r-knitr
+           r-plyr
+           r-purrr
+           r-r-utils
+           r-readr
+           r-rvest
+           r-s4vectors
+           r-stringr
+           r-summarizedexperiment
+           r-tcgabiolinksgui-data
+           r-tibble
+           r-tidyr
+           r-xml
+           r-xml2))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks")
+    (synopsis "Integrative analysis with GDC data")
+    (description
+     "The aim of TCGAbiolinks is:
+
+@enumerate
+@item facilitate GDC open-access data retrieval;
+@item prepare the data using the appropriate pre-processing strategies;
+@item provide the means to carry out different standard analyses, and;
+@item to easily reproduce earlier research results.
+@end enumerate
+
+In more detail, the package provides multiple methods for analysis (e.g.,
+differential expression analysis, identifying differentially methylated
+regions) and methods for visualization (e.g., survival plots, volcano plots,
+starburst plots) in order to easily develop complete analysis pipelines.")
+    (license license:gpl3+)))
+
 (define-public r-tximeta
   (package
     (name "r-tximeta")
-    (version "1.10.0")
+    (version "1.12.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "tximeta" version))
        (sha256
         (base32
-         "0ipgpcl93cac4qff6lp9x2l3gav5kb1x1d56g32h09hlm797rvvh"))))
+         "1lm2r64d6sdfzvxcabgs0214cdc5dl9pfx562acjcxz5mb101g9g"))))
     (properties `((upstream-name . "tximeta")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationhub" ,r-annotationhub)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-biostrings" ,r-biostrings)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-jsonlite" ,r-jsonlite)
-       ("r-matrix" ,r-matrix)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-tibble" ,r-tibble)
-       ("r-tximport" ,r-tximport)))
+     (list r-annotationdbi
+           r-annotationhub
+           r-biocfilecache
+           r-biostrings
+           r-ensembldb
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-iranges
+           r-jsonlite
+           r-matrix
+           r-s4vectors
+           r-summarizedexperiment
+           r-tibble
+           r-tximport))
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/mikelove/tximeta")
     (synopsis "Transcript quantification import with automatic metadata")
     (description
@@ -14782,3 +15235,41 @@ and other associated metadata.  De novo transcriptomes can be linked to the
 appropriate sources with linkedTxomes and shared for computational
 reproducibility.")
     (license license:gpl2)))
+
+(define-public r-phyloseq
+  (package
+    (name "r-phyloseq")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "phyloseq" version))
+       (sha256
+        (base32 "0k0aj8f7g1vr7l0qcc507b3w67zc1k9x7sdblm7mjb20zqr3916s"))))
+    (properties `((upstream-name . "phyloseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ade4
+           r-ape
+           r-biobase
+           r-biocgenerics
+           r-biomformat
+           r-biostrings
+           r-cluster
+           r-data-table
+           r-foreach
+           r-ggplot2
+           r-igraph
+           r-multtest
+           r-plyr
+           r-reshape2
+           r-scales
+           r-vegan))
+    (native-inputs
+     (list r-knitr))
+    (home-page "https://github.com/joey711/phyloseq")
+    (synopsis "Handling and analysis of high-throughput microbiome census data")
+    (description
+     "Phyloseq provides a set of classes and tools to facilitate the import,
+storage, analysis, and graphical display of microbiome census data.")
+    (license license:agpl3)))