diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 819 |
1 files changed, 683 insertions, 136 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d2eb9a0daf..fe446df67a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -33,6 +33,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) @@ -1481,6 +1482,47 @@ genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.") (license license:gpl3+))) +(define-public r-hdcytodata + (package + (name "r-hdcytodata") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HDCytoData" version 'experiment)) + (sha256 + (base32 + "1fn8q6ds10z3ymdarkfyh88pcqnrry9yhzammp84vf86f0bl8mrc")))) + (properties `((upstream-name . "HDCytoData"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ + (setenv "HOME" "/tmp"))) + (add-after 'unpack 'avoid-internet-access + (lambda _ + (setenv "GUIX_BUILD" "yes") + (substitute* "R/zzz.R" + (("createHubAccessors.*" m) + (string-append + "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m "}")))))))) + (propagated-inputs + (list r-experimenthub r-flowcore r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/lmweber/HDCytoData") + (synopsis + "Set of high-dimensional flow cytometry and mass cytometry benchmark datasets") + (description + "HDCytoData contains a set of high-dimensional cytometry benchmark +datasets. These datasets are formatted into SummarizedExperiment and flowSet +Bioconductor object formats, including all required metadata. Row metadata +includes sample IDs, group IDs, patient IDs, reference cell population or +cluster labels and labels identifying spiked in cells. Column metadata +includes channel names, protein marker names, and protein marker classes.") + (license license:expat))) + (define-public r-italicsdata (package (name "r-italicsdata") @@ -2056,6 +2098,96 @@ impute GReX can be trained with a training dataset where the real total expression values are known.") (license license:gpl3))) +(define-public r-affyilm + (package + (name "r-affyilm") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affyILM" version)) + (sha256 + (base32 "0i2hjaqjz06ym5kbw5da1h3cahc630mjwljsji1l2ks0gjcipll0")))) + (properties `((upstream-name . "affyILM"))) + (build-system r-build-system) + (propagated-inputs + (list r-affxparser + r-affy + r-biobase + r-gcrma)) + (home-page "https://bioconductor.org/packages/affyILM") + (synopsis + "Linear model of background subtraction and the Langmuir isotherm") + (description + "The affyILM package is a preprocessing tool which estimates gene +expression levels for Affymetrix Gene Chips. Input from physical chemistry is +employed to first background subtract intensities before calculating +concentrations on behal of the Langmuir model.") + (license license:gpl3))) + +(define-public r-affylmgui + (package + (name "r-affylmgui") + (version "1.72.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affylmGUI" version)) + (sha256 + (base32 "0jds73pxqf522wcg8qd4b4k1qbhn51av5md1nhgcdnb6is0lzvxi")))) + (properties `((upstream-name . "affylmGUI"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-affyio + r-affyplm + r-annotationdbi + r-biocgenerics + r-biocmanager + r-gcrma + r-limma + r-r2html + r-tkrplot + r-xtable)) + (home-page "https://bioinf.wehi.edu.au/affylmGUI/") + (synopsis "GUI for limma package with Affymetrix microarrays") + (description + "This package provides a @acronym{GUI, Graphical User Interface} for +analysis of Affymetrix microarray gene expression data using the affy and +limma packages.") + (license license:gpl2+))) + +(define-public r-affyplm + (package + (name "r-affyplm") + (version "1.74.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affyPLM" version)) + (sha256 + (base32 "0f0faxjzlg0znhjfvf1490yc54npkx659jx76cddm5hk7q0blv3v")))) + (properties `((upstream-name . "affyPLM"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-affy + r-biobase + r-biocgenerics + r-gcrma + r-preprocesscore + r-zlibbioc)) + (home-page "https://github.com/bmbolstad/affyPLM") + (synopsis "Methods for fitting probe-level models") + (description + "The affyPLM provides a package that extends and improves the +functionality of the base affy package. For speeding up the runs, it includes +routines that make heavy use of compiled code. The central focus is on +implementation of methods for fitting probe-level models and tools using these +models. @acronym{PLM, probe-level models} based quality assessment tools are +also provided.") + (license license:gpl2+))) + (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") @@ -2575,6 +2707,57 @@ Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.") (license license:artistic2.0))) +(define-public r-annotationhubdata + (package + (name "r-annotationhubdata") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationHubData" version)) + (sha256 + (base32 "0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95")))) + (properties `((upstream-name . "AnnotationHubData"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'install 'set-home + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-annotationdbi + r-annotationforge + r-annotationhub + r-biobase + r-bioccheck + r-biocgenerics + r-biocmanager + r-biocviews + r-biostrings + r-dbi + r-futile-logger + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-jsonlite + r-organismdbi + r-rcurl + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AnnotationHubData") + (synopsis "Transform public data resources into Bioconductor data structures") + (description + "This package provides tools to acquire, annotate, convert and store data +for use in Bioconductor’s AnnotationHub.") + (license license:artistic2.0))) + (define-public r-anvil (package (name "r-anvil") @@ -2774,18 +2957,19 @@ data.") (define-public r-alpsnmr (package (name "r-alpsnmr") - (version "4.0.2") + (version "4.0.4") (source (origin (method url-fetch) (uri (bioconductor-uri "AlpsNMR" version)) (sha256 (base32 - "1y4qqc6l8flv5ns4qwzjwmcykm6zcm4jg097mn8xyp7mnxymy7pl")))) + "19j97qsa1vnxw05dlllbwzdap0xgnmgxyqbi5dy8w2ppwdzxgsfv")))) (properties `((upstream-name . "AlpsNMR"))) (build-system r-build-system) (propagated-inputs (list r-baseline r-biocparallel + r-cli r-dplyr r-fs r-future @@ -3224,13 +3408,13 @@ variant.") (define-public r-atena (package (name "r-atena") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "atena" version)) (sha256 (base32 - "1a3qv66caz2pg67ff9c5424pygsgqnfx67ybzc3zkzaw4fj8cp54")))) + "0j6jq1cll8440i2srmy4lbvvyqawailk9byl9bnnzln1mdgys8r7")))) (properties `((upstream-name . "atena"))) (build-system r-build-system) (propagated-inputs @@ -3242,6 +3426,7 @@ variant.") r-genomicranges r-iranges r-matrix + r-matrixstats r-rsamtools r-s4vectors r-scales @@ -3518,13 +3703,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.0.5") + (version "3.0.8") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "12rcbspy4ly714cyxbgd5v2m92vasksxm19m6hd4avasrhcr4d6l")))) + "072rys45f9nl4b2dq559qakjcp2990ncdw49j49761izxgc7byzs")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -3561,13 +3746,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "0dbiz7zgdl3bqrwf4ffb73sc2dd8ygh76fakx5887a14azj8pk8x")))) + "11w0azh2g0y331imqpllnb0csjxf3gs1767cc67c1zp0ykg6yq8l")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs @@ -4440,14 +4625,14 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-infercnv (package (name "r-infercnv") - (version "1.14.0") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "11hgw6c67gd3ih5q14a520sjmnlv56qw19z0i6s5pz2slmgflpry")))) + "04m51jdahhmj31cs2af9il5zijkpb255f9p06i8ga0v3g79gj1bp")))) (properties `((upstream-name . "infercnv"))) (build-system r-build-system) (inputs (list python)) @@ -4717,14 +4902,14 @@ mapping.") (define-public r-nmf (package (name "r-nmf") - (version "0.25") + (version "0.26") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 - "0kdl7yz4v7pms6y2lff4x5w7pwkx54488qx0v539qmvcbxv1if98")))) + "1h1fpjnj6vjvi9ygxpfxs8k5bhly0aflr54zj88khgzkylp5ci4d")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs @@ -4747,7 +4932,7 @@ mapping.") r-stringr)) (native-inputs (list r-knitr)) - (home-page "http://renozao.github.io/NMF") + (home-page "https://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description "This package provides a framework to perform Non-negative Matrix @@ -4999,13 +5184,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.60.0") + (version "1.60.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1srv0jizmwgmsmgb9cfgy5nbgd3jsgxgzzax6wfsahckb5zihrqp")))) + "1c7f2vgdnh99zp83pvmghb7l0rihdijlhdj6ff992h7wrrha8lhg")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -5054,14 +5239,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.40.0") + (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "15shh8rmcx69g3zd256720vh0c3qbly5zrvwm463dws41cjla48x")))) + "16wdcl56d5i8wrmin610kzs9ldy7h9w5fbnysjb1crkcgbikq1yy")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -5288,13 +5473,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.32.5") + (version "1.32.6") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1yd6ln9cl3dcvfziar52fkvqi2lzm31l7j21r1rwl1mpkz0xapir")))) + "1aq3b5fjs8j0d6nf3992a6gnzvmmaxbbkrj1im0k6ppsqac6dlj0")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -5409,13 +5594,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.66.2") + (version "1.66.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "0p75c52sw464bdqz7dyda9h8k2wsxdpdxxhya5awh977xaly90pf")))) + "1ps7s6i9mv8ys8k2xw8fdkh2rl2n3kcf2q4zsz6kcz5qpav95ys6")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -5581,6 +5766,57 @@ provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on r-complexheatmap from +;; Bioconductor. +(define-public r-conos + (package + (name "r-conos") + (version "1.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "conos" version)) + (sha256 + (base32 "1wdhb3jxh4id6xaghawzip8s264g9jxp4i5xy7jfhi67yfxszx6w")))) + (properties `((upstream-name . "conos"))) + (build-system r-build-system) + (propagated-inputs + (list r-abind + r-complexheatmap + r-cowplot + r-dendextend + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-igraph + r-irlba + r-leidenalg + r-magrittr + r-matrix + r-n2r + r-r6 + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppprogress + r-reshape2 + r-rlang + r-rtsne + r-sccore)) + (home-page "https://github.com/kharchenkolab/conos") + (synopsis "Clustering on network of samples") + (description + "This package wires together large collections of single-cell RNA-seq +datasets, which allows for both the identification of recurrent cell clusters +and the propagation of information between datasets in multi-sample or +atlas-scale collections. Conos focuses on the uniform mapping of homologous +cell types across heterogeneous sample collections. For instance, users could +investigate a collection of dozens of peripheral blood samples from cancer +patients combined with dozens of controls, which perhaps includes samples of a +related tissue such as lymph nodes.") + (license license:gpl3))) + (define-public r-copywriter (package (name "r-copywriter") @@ -5655,14 +5891,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.38.2") + (version "1.38.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1m81yvcl63h5m7kbbxpjk7hzygxmn4l9mlgqrdmnnls56183h3b4")))) + "0kryg9jb6zl4zj1wx09rmljqlhr5vdbcmdnri4q91jpggsaj9nxm")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -5887,18 +6123,18 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.40.1") + (version "3.40.2") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1a0rmczlqmqmip2ix28m4iwcpfj04p6nrcl562bjgaifvgyjqhzg")))) + "0ds34b135qd63dh3cxkp8b28270m50bn1njwr49b8svgcgzz9x09")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit r-rcpp)) - (home-page "http://bioinf.wehi.edu.au/edgeR") + (home-page "https://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") (description "This package can do differential expression analysis of RNA-seq expression profiles with biological replication. It implements a range @@ -6012,14 +6248,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.80.2") + (version "1.80.3") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0f25z0hqmrkimv14j03pgjsxpq5rz9ymk151rlg4j4vpc06n73cq")))) + "047p84qxfqqm0d0ik7fxcs37fmg0yazsn9rz7h4g24cksb45p689")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -6102,13 +6338,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.34.6") + (version "1.34.9") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "123kp69fmy5pbqh0j6qxdkvkm4g9pdwzms01i8qnix3m1b9j597w")))) + "0mn9ddm2xwc2b7zg0n9a056jcr61jv6v8jacxm3q8qmz6r30kfrb")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -6129,13 +6365,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0y9yjyzch0cn2j4yrwfp0z8qw3yqvl8h1dlrl7ylzy9mwsqc6wg5")))) + "1c784ic85v64gflwwk22dh3f0m60q3z6y23d9jy3w8ydhda6gw0s")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -6162,13 +6398,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.50.3") + (version "1.50.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "14pn7lngayascj5k84g2g748assbivpiakss247cdj9ngzx5sfwz")))) + "1qsr433nh225pk5ngsrjrf2rfv7ynq4c8qsjfjr7khy2z9czlg6n")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -6427,13 +6663,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.72.2") + (version "1.72.3") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "1k697pqlkrwmfszipl9irbzmwhk1vz97j3rh0k5nj2mrj3dr71mv")))) + "1qq80za9bkg0wqnlckvahnjz08xacwvpnflwnrmwr2xg0ifkis38")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -6496,13 +6732,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lfa (package (name "r-lfa") - (version "1.28.1") + (version "1.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "0047wspvarbnbawrwvfjfz5y6i36l2r2k2501zjya09rjpiq101m")))) + (base32 "0z8aa2435f7v2l6zwv47v2a6p9hal156dsh8v1iri233d1qx7fax")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) @@ -6517,15 +6753,15 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.54.0") + (version "3.54.2") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1jy75nbkhl0kgv4gw88acx58r9f1kywrd36405x6g05xy05bprma")))) + "1qch34znld9i8sy1xwpy23z2zs07nj39wkfmgfi7qw141vn6gr8b")))) (build-system r-build-system) - (home-page "http://bioinf.wehi.edu.au/limma") + (home-page "https://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") (description "This package can be used for the analysis of gene expression studies, especially the use of linear models for analysing designed experiments @@ -6533,6 +6769,73 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-maaslin2 + (package + (name "r-maaslin2") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Maaslin2" version)) + (sha256 + (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89")))) + (properties `((upstream-name . "Maaslin2"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'check 'remove-timestamps + (lambda _ + (with-directory-excursion + (string-append #$output "/site-library/Maaslin2/doc/demo_output/") + ;; Delete this log file with timestamps. + (delete-file "maaslin2.log") + ;; Replace PDF timestamps with an arbitrary fixed timestamp. + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* (find-files "." "\\.pdf$") + (("/CreationDate \\(D:.*\\)") + "/CreationDate (D:20230301143558)") + (("/ModDate \\(D:.*\\)") + "/ModDate (D:20230301143558)"))))))))) + (propagated-inputs + (list r-biglm + r-car + r-chemometrics + r-cplm + r-data-table + r-dplyr + r-edger + r-ggplot2 + r-glmmtmb + r-hash + r-lme4 + r-lmertest + r-logging + r-lpsymphony + r-mass + r-mumin + r-metagenomeseq + r-optparse + r-pbapply + r-pcapp + r-pheatmap + r-pscl + r-rmarkdown + r-robustbase + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "http://huttenhower.sph.harvard.edu/maaslin2") + (synopsis + "Multivariable association discovery in population-scale meta-omics studies") + (description + "MaAsLin2 is comprehensive R package for efficiently determining multivariable +association between clinical metadata and microbial meta'omic features. This +package relies on general linear models to accommodate most modern epidemiological +study designs, including cross-sectional and longitudinal, and offers a variety +of data exploration, normalization, and transformation methods.") + (license license:expat))) + (define-public r-made4 (package (name "r-made4") @@ -6644,6 +6947,40 @@ experiments.") and visualizaton of alternative splicing events generated by rMATS.") (license license:expat))) +(define-public r-metagenomeseq + (package + (name "r-metagenomeseq") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "metagenomeSeq" version)) + (sha256 + (base32 "01wjw4kcm8ysa5sn3cqg4a9i5pyksnwmbdqp5fr6n2l9hllkc9jy")))) + (properties `((upstream-name . "metagenomeSeq"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-foreach + r-glmnet + r-gplots + r-limma + r-matrix + r-matrixstats + r-rcolorbrewer + r-wrench)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/HCBravoLab/metagenomeSeq") + (synopsis "Statistical analysis for sparse high-throughput sequencing") + (description + "MetagenomeSeq is designed to determine features (be it @acronym{OTU, +Operational Taxanomic Unit}, species, etc.) that are differentially abundant +between two or more groups of multiple samples. This package is designed to +address the effects of both normalization and under-sampling of microbial +communities on disease association detection and the testing of feature +correlations.") + (license license:artistic2.0))) + (define-public r-metaneighbor (package (name "r-metaneighbor") @@ -6727,6 +7064,75 @@ resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.") (license license:artistic2.0))) +(define-public r-mmuphin + (package + (name "r-mmuphin") + (version "1.12.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MMUPHin" version)) + (sha256 + (base32 "0vpap3avmrjy187s3dva6f008al6d935kpdf816xzl5gxl7zvf62")) + ;; Delete generated files. + (snippet + '(for-each delete-file + '("inst/doc/MMUPHin.R" + "inst/doc/MMUPHin.html"))))) + (properties `((upstream-name . "MMUPHin"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-includes + (lambda _ + (substitute* "inst/doc/MMUPHin.Rmd" + (("\\.\\./man/figures") + (string-append (getcwd) "/man/figures")) + (("bibliography: references.bib") + (string-append "bibliography: " + (getcwd) "/vignettes/references.bib"))))) + ;; Maaslin2 generates log files with timestamps. We don't need to + ;; keep them. The generated PDF files also contain timestamps, so + ;; we replace them with arbitrary fixed timestamps. + (add-after 'check 'make-reproducible + (lambda _ + (for-each delete-file + (find-files #$output "maaslin2.log")) + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* (find-files #$output "\\.pdf$") + (("/CreationDate \\(D:.*\\)") + "/CreationDate (D:20230301143558)") + (("/ModDate \\(D:.*\\)") + "/ModDate (D:20230301143558)")))))))) + ;; The DESCRIPTION file says that glpk is needed, but this package does + ;; not seem to reference the library directly. + (propagated-inputs + (list r-cowplot + r-biocstyle + r-dplyr + r-fpc + r-ggplot2 + r-igraph + r-maaslin2 + r-metafor + r-stringr + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/MMUPHin") + (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome") + (description + "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. +It has function interfaces for: +@itemize +@item covariate-controlled batch- and cohort effect adjustment; +@item meta-analysis differential abundance testing; +@item meta-analysis unsupervised discrete structure (clustering) discovery; +@item meta-analysis unsupervised continuous structure discovery. +@end itemize") + (license license:expat))) + (define-public r-motifrg (package (name "r-motifrg") @@ -6757,14 +7163,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-muscat (package (name "r-muscat") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 - "07b1z8rd0zibmv3rm4zggjf49lh37p2bp1h919zcw3n0fy2hax1k")))) + "061dgs3ygvr4vrc6mrmikqn4a7a5qajn7k8crbskdkg4svg8qv1a")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs @@ -6807,14 +7213,14 @@ platform that mimics both single and multi-sample scRNA-seq data.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.8.0") + (version "3.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "071s1hfxln8zdr303g0ifmajd3kcfxxb6dds0pz67chc2gmgnd9q")))) + "0d0fsc4x8psfd93asi2d5kq1888s963d3s8kcihd5knqah000mh8")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -6850,6 +7256,37 @@ characterization and visualization of a wide range of mutational patterns in SNV base substitution data.") (license license:expat))) +(define-public r-msa + (package + (name "r-msa") + (version "1.30.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "msa" version)) + (sha256 + (base32 + "064hmry0zhmpchxgjsw0krsybr9v9gbsz26zmj2a39pg1nggwbq4")))) + (properties `((upstream-name . "msa"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-iranges + r-rcpp + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "http://www.bioinf.jku.at/software/msa/") + (synopsis "Multiple sequence alignment") + (description + "The msa package provides a unified R/Bioconductor interface to the +multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. +All three algorithms are integrated in the package, therefore, they do not +depend on any external software tools and are available for all major +platforms. The multiple sequence alignment algorithms are complemented by a +function for pretty-printing multiple sequence alignments using the LaTeX +package TeXshade.") + (license license:gpl2+))) + (define-public r-msnbase (package (name "r-msnbase") @@ -7038,13 +7475,13 @@ previously been used in XCMS.") (define-public r-numbat (package (name "r-numbat") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "numbat" version)) (sha256 (base32 - "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb")))) + "06qq7i8k1mi7yg1irfbk3d2fmk7awvzj7h7r54hnr6pzywk7nmhc")))) (properties `((upstream-name . "numbat"))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -7172,6 +7609,32 @@ annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.") (license license:artistic2.0))) +(define-public r-oscope + (package + (name "r-oscope") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Oscope" version)) + (sha256 + (base32 + "0454f9yc0jmg3mcq9264wb5v2n8n0kaf801hlvsiy1xa3baj3h29")))) + (properties `((upstream-name . "Oscope"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) + (home-page "https://bioconductor.org/packages/Oscope") + (synopsis + "Oscillatory genes identifier in unsynchronized single cell RNA-seq") + (description + "Oscope is a oscillatory genes identifier in unsynchronized single cell +RNA-seq. This statistical pipeline has been developed to identify and recover +the base cycle profiles of oscillating genes in an unsynchronized single cell +RNA-seq experiment. The Oscope pipeline includes three modules: a sine model +module to search for candidate oscillator pairs; a K-medoids clustering module +to cluster candidate oscillators into groups; and an extended nearest +insertion module to recover the base cycle order for each oscillator group.") + (license license:asl2.0))) + (define-public r-pcaexplorer (package (name "r-pcaexplorer") @@ -7788,13 +8251,13 @@ method applicable to massive single-cell datasets (>10,000 cells).") (define-public r-scmap (package (name "r-scmap") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "0rq185ynk874vgw4a5s2n92381dj6kxxnx2fcx2v7b2ahr3ybys7")))) + (base32 "00zqvjfn1pqza5gl3jfr10fvcrq6gpw9hfjcxjsm4f5p7ldnhpw0")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -8192,13 +8655,13 @@ Biology at (define-public r-stringdb (package (name "r-stringdb") - (version "2.10.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "1md79vx4270wgh07g3m1mypdki1b9d4a558zxplcalwppqh0dsmp")))) + (base32 "0qpss8fcf8ll47jv45ypsqd9jf7ajdiya7w4mw1wysk76spcwllm")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs @@ -8428,14 +8891,14 @@ of gene-level counts.") (define-public r-valr (package (name "r-valr") - (version "0.6.6") + (version "0.6.7") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 - "0w3j8fkssp9s4ybaw8hvqbmsh5m991xkgr4nji3zar2pgmgk3qph")))) + "1s8bjbban2a3cqhwgykmhkv5b748nscamfbv67v4cppjbdvlhb5s")))) (build-system r-build-system) (propagated-inputs (list r-broom @@ -8461,13 +8924,13 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.44.0") + (version "1.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "08rm27jcx6amawqdh59291r0qzkr5cdhbhm0xbjbd5mvdpp1icl8")))) + "13zim7dglsd5w39v22d2qa3d1h5dx33c1r4fz3vzri64kac0lhzx")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs @@ -8776,14 +9239,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.62.1") + (version "1.62.2") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "1rhzav57d092ip9qjsmskj3l8h4xyq8cpa2a2jl8g32fwh0dyvsz")))) + "19n0nvgyv2hzzcla93w2bzxvfdqg6walh0s1yykwl5b7ni4cazg9")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) @@ -8948,14 +9411,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.8.3") + (version "3.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "039gy9ll6ingh3y5h2hp3rhbh2imaryjxzgf8ysk87irlbpnx1qs")))) + "1gil19qk4wc695sl7r789xnqyv748n4jdhaighkjy5hfp9xaaax7")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -9512,14 +9975,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "14fb780f2g24ay28dy9xkmfziavbkj75v4vc2cmqbxfdsfp4yn0w")))) + "1nk8jhabbrirpyjd1wdy2fjk8y2qi1bsjmgqzh0qi1c83n0ccz5d")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -9666,13 +10129,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "1qxzbh5i208cpghmysailachj8xpx4g4iqk8552xjpjkn54pkpbd")))) + "1ihjqzdhx6k99gdd4556xxn9822sblg6vmblcmbzml01bhv6xzar")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs @@ -9735,7 +10198,7 @@ in omics data.") (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) - (home-page "http://www.genopolis.it") + (home-page "https://www.genopolis.it") (synopsis "Detect differential expression in microarray and proteomics datasets") (description "The Power Law Global Error Model (PLGEM) has been shown to faithfully @@ -10193,14 +10656,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.72.2") + (version "1.72.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "1f6ilfwhli7bdnr48y2ijdydvw7kjbyz701kgbsw3w7inr6x6ayr")))) + "1kxzrny19dqd9pqj27vzr15i071sl8ivznpfd6zlqhcymlcsq7nw")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -10351,14 +10814,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.26.2") + (version "1.26.3") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "167zpf7k7gn7gw2cxkqx89y322qinyzjr1naracp5axj4q2qagm3")))) + "0iqc6km4pw50li2q35km8jpa0p3i6a6way910wcz56yd2jjbjyz5")))) (build-system r-build-system) (arguments (list @@ -10528,16 +10991,28 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "133ijkw5sd0gl38dfr7qfqvvp2df7lg6j8vkvy54zlpamkg6l2x1")))) + "1c0lc4abnb859x481ky6d3kc9zzxwvf4kqgwxyqapc4g72b4vh65")) + (snippet + '(delete-file "docs/jquery.sticky-kit.min.js")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (invoke "esbuild" + (assoc-ref inputs "js-jquery-sticky-kit") + "--minify" + "--outfile=docs/jquery.sticky-kit.min.js")))))) (propagated-inputs (list r-abind r-biobase @@ -10552,7 +11027,16 @@ the numbers of cells across batches.") r-stringr r-summarizedexperiment)) (native-inputs - (list r-knitr)) + `(("esbuild" ,esbuild) + ("js-jquery-sticky-kit" + ,(origin + (method url-fetch) + (uri + "https://cdn.jsdelivr.net/gh/leafo/sticky-kit@v1.1.2/jquery.sticky-kit.js") + (sha256 + (base32 + "17c3a1hqc3ybwj7hpw8prazajp2x98aq7nyfn71h6lzjvblq297g")))) + ("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/MAST/") (synopsis "Model-based analysis of single cell transcriptomics") (description @@ -11240,14 +11724,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.22.1") + (version "2.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "16d7viyidqbsy3mbr2cpq9p291yf362a4blhvs05qxcwm3fjllij")))) + "0snsvyy8d85panizm848mrmjpgyc06iqp39d19rny3fphq3adwn5")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -11342,14 +11826,14 @@ surface of a flowcell.") (define-public r-mutoss (package (name "r-mutoss") - (version "0.1-12") + (version "0.1-13") (source (origin (method url-fetch) (uri (cran-uri "mutoss" version)) (sha256 (base32 - "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298")))) + "0hgi9wpy3ai23dk6cdba6r118vvmgw210racsg3n1p24rv6ny3xn")))) (properties `((upstream-name . "mutoss"))) (build-system r-build-system) (propagated-inputs @@ -11588,14 +12072,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.66.1") + (version "1.66.2") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1ln1n4zwmjw1ils45vix93q3h19xlg4q894yhhxkphgyj0qcy00b")))) + "0k86hlz7zbbw7559bd2sl59pr441kihgwvg8nr75mj8d50n783sy")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -11750,14 +12234,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.6.0") + (version "4.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "0fm2cz2464xh075p4yl6bha9m6didc41ng4a3flkw1f1cvvpi4g0")))) + "017wqd1nwcrhbpzvhcqc3if0n084dspq7y3fbc5dnik6yi04q0dg")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -11788,13 +12272,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.18.1") + (version "2.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "1f3f56d88yiqyj45rhcwqb04wbxr9m4fxhbbckw1j7nykm8100ps")))) + "03flqixy6flaqynpaf3nz42kwf71v53wxs5vywj3bqmninzywmbk")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -12217,12 +12701,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.12.0") + (version "2.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0lq79as9gb48hf3v2xj895s0nsjr37fqah4p405kdybzry56gvrq")))) + (base32 "073xv26yaksqa0j2vyqf8ak5yqsxg5s86izdlmlwdidnxdnd16si")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -13004,14 +13488,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.64.0") + (version "1.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0l86gwq073nbx973v99b0lr9cz0pb72c4asmgj5w16jykicrnxn9")))) + "0p8cd4r3c8va5gybs1vlm3kn7jcg1xg529hvvg27fybb3g91nvqg")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -13279,14 +13763,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.4.0") + (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "05cczwkhv7kfnhlr0qznk6vdjncaj907895923f8mwx4j4cy5gcz")))) + "0cbm6q4v9ddyx4gnw2p47ssyhnmjfxahvzbzwjzn0my3ixssy0aj")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs @@ -13361,14 +13845,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.6.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0skrvmkm6ch8gbpdi4wr59zk5vxzxs7cyqvz3jhki9d8w492wylg")))) + "16316a5pgyl5rppyviibf6z3k3m7xmvqyylf1kxdpg0avs6dk8w7")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -13394,14 +13878,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.34.2") + (version "1.34.3") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "05y4jmbf8sxl32f3g5lw9ycxky0rw69gax3n2z0kif7xcb5qf3qv")))) + "0d7qsdjry5avflrvgjj287xqn9dr54pqiqvpgywzdmdwn82m0dfp")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -13834,14 +14318,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.12.2") + (version "2.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "1gvd8vmglvzc3bixqxrm4k7yikl2as5l4x6bvvvnwsgx2i7vz7dm")))) + "0lhmva8yghlbb44h1fvbcqfp8zvdn4pd4nwyd2drh6b271f8qjdd")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -13952,23 +14436,20 @@ of the analyses while minimizing technical noise.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.10.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "1y06x7z3p938kfvjx6zqab9hh1xzlrlhdxczyprx7lsd34ylz46n")))) + "0rgqlqasil75b03c8c4nyg71ybysrsbqb0bwk6hbnaw8rljxdmi5")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-bh - r-rcpp - r-rcpparmadillo - r-rcppparallel r-rhdf5lib r-rprotobuflib)) (home-page "https://bioconductor.org/packages/cytolib/") @@ -14594,14 +15075,14 @@ expression space.") (define-public r-cicero (package (name "r-cicero") - (version "1.16.0") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0grzp9k06dz04bw07nf9qka19mara1kplyd24y8mg8208wk949f6")))) + "1gf359x6lvm3kc4mlsh7vxf8lmvhp080fi0cksvb4mcypafp67cv")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -14661,14 +15142,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.12.0") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "07l8vaqbw36hvs8pyn1gk6dglnmkcmbafvd4rdrhg2wqwnlpsf40")))) + "1i954hn7xyajpkg4fks04jd86flcmy2326nzpmxgy8h69jkzdc8q")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -15249,14 +15730,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.28.1") + (version "1.28.9") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0ypw3ckaf4qll83rl2bjzfc7g2m4v0n2mq645ppyfga8wv8kwssy")))) + "1al7wkbv26gldba61gq80c3mznsxwr7z5njv2s0lb7hnll9bscar")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -16143,13 +16624,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.34.2") + (version "1.34.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1zj43kbzvi2ws8c182fp6vn5r6iiqsr6p2iyy3k8n3ifm2acqw2h")))) + "00z2l5jnc028bmd3rl3qmgkd6k1mfa4p68kls34mkn29ic9ls22m")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -16218,13 +16699,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.66.2") + (version "1.66.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0fdxlixwf4d3p1prq37cgfvaiym44h2yd4bym6wp4dl8h648v99y")))) + "0ddxz7a8csf1l4srnjcgg5ps00fkcbv99y5wa0yrl6p9zr2d61qy")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -16417,16 +16898,50 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1av7vnw6z9cw7j4d3vpi8mfs5h4pn4yr2wc8ybg7ad1d686ah845")))) + "0cl88adkbxv7sz07b8h5qpwwkwg85jx6xjinkd0yjac4xm7s4lyf")) + (snippet + '(for-each delete-file + '("inst/htmlwidgets/lib/bioc_explore/bootstrap.min.js" + "inst/htmlwidgets/lib/bioc_explore/d3.v3.min.js" + "inst/htmlwidgets/lib/bioc_explore/jquery-2.2.4.min.js" + "inst/htmlwidgets/lib/bioc_explore/underscore-min.js"))))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/bioc_explore" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-bootstrap") + "bootstrap.min.js") + (,(assoc-ref inputs "js-d3") + "d3.v3.min.js") + (,(assoc-ref inputs "js-jquery") + "jquery-2.2.4.min.js") + (,(search-input-file inputs "/underscore.js") + "underscore-min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets))))))))) (propagated-inputs (list r-biocfilecache r-biocmanager @@ -16450,7 +16965,40 @@ gene selection, testing relationships, and so on.") r-tibble r-xml2)) (native-inputs - (list r-knitr)) + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("js-bootstrap" + ,(origin + (method url-fetch) + (uri + "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.6/dist/js/bootstrap.js") + (sha256 + (base32 + "07fm28xbkb7a5n7zgmfxgbl2g5j010r4gvc54y79v1f119s3kz6y")))) + ("js-d3" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v3.js") + (sha256 + (base32 + "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-2.2.4.js") + (sha256 + (base32 + "18m6qmmsm3knvybf6gpwmwiasi05y98gcpb364if8qh94gv90gl9")))) + ("js-underscore" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jashkenas/underscore") + (commit "1.8.3"))) + (file-name (git-file-name "underscorejs" "1.8.3")) + (sha256 + (base32 + "1r54smxpl3c6jg6py29xjc2l1z49rlm1h48vr9i57wvnkbnbl0h3")))))) (home-page "https://github.com/seandavi/BiocPkgTools") (synopsis "Collection of tools for learning about Bioconductor packages") (description @@ -16805,14 +17353,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.60.1") + (version "1.60.2") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1rwr31jp4dh3xcfx1kx8rz5xvyx1mrwy85hqrjrfr4m6h0qv28k1")))) + "0ikxikmz9dy09g726q1wygymm6z2imlgfiizkgh1cl4s0m35fbbd")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -16826,13 +17374,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.36.1") + (version "0.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "16lssnmhy3klqp4sw1328f38cixkjh9317gdyikcrmsbcwg2ak6v")))) + "131cg5fzrqgyp4kv260yn8hpr0zv5mxjhdnpl50ydgc2k0l43d38")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -16855,14 +17403,14 @@ S4Vectors package itself.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.71") + (version "1.72-1") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91")))) + "1p3zsl5r6l5r6ylnrxmbxjpim5qgmncgdjcgn5j69rzk3rv85gqx")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -16931,13 +17479,13 @@ objects from the @code{graph} package.") (define-public r-fishpond (package (name "r-fishpond") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "fishpond" version)) (sha256 (base32 - "112jd53wbiv1w0n8dc4qn6257wbbbg5i20s9wlvaw98jma94afa6")))) + "0kc1xzq03kz548rfinxhc7gxm6021502b6v7bg2har0aq4vx79ml")))) (properties `((upstream-name . "fishpond"))) (build-system r-build-system) (inputs (list zlib)) @@ -16950,7 +17498,6 @@ objects from the @code{graph} package.") r-matrix r-matrixstats r-qvalue - r-rcpp r-s4vectors r-singlecellexperiment r-summarizedexperiment @@ -17336,13 +17883,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "1nhhpqhpvmw6b0nwxdwsjnakmfpxzpii8fmabwwg9bk8ni3zj5dq")))) + (base32 "034in81lsdxa8j1na2zymck2y67235qprin8hak3dwa7lwzbm12z")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -17383,14 +17930,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "1y9c9wf3009w4qh03zpsmc0ff0nkzal673a4nql5c11cn55sza2g")))) + "1xwa6ncmqp21a4zx1dbs9p9b9rqbxhdgq2279mj4yl0gnpyqr9d7")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -17443,14 +17990,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.8.3") + (version "1.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1wgh28rj8m5dz89s9y4rzfy68d8ign6pcnnwj9g7h4sc3jfsg56i")))) + "04257gl995r575md1n3h2gy502yi6c8x3352l96mib7rdv4yg53f")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -17523,14 +18070,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.26.1") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1sqc8pf1qzm24kf1l45da12wbzv0nxsy6l3v9fc8srmnvk37p04p")))) + "0r80k4dsk609l9ha1jl64yhpwnf0x37i28k9largqsffsl6hw0fy")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -18042,14 +18589,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.42.0") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "09j94kk3dd3bbfw6a2l14i7vd4rh11g9lxhw4zsm15vg71cm1lv9")))) + "01qs60sdh7c8cxkv3qbfcfwpjhab88j872va50fi95xsqnmj5isa")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -18211,14 +18758,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.7-1") + (version "2.7-3") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr")))) + "02qmp3ky671fkpjq1vcb083zzvfn5gkf69rhvdlvg7siy5wrjll3")))) (build-system r-build-system) (inputs (list gsl)) @@ -18766,14 +19313,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.8.1") + (version "1.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "0zmiaixknwxv72l4fygrn0qr3mvl7kqfbqgflnavs0wxx6xdjqgn")))) + "0h1cwir6m3zg728vdxxz03rfwysw92m9djdfj0vayixli2j4xz5a")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments @@ -19545,14 +20092,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0v1s5ssinyrizpg2i88dn2ckzs4i16hjfg2pzxhal3ypsiw24qna")))) + "15qf8s9akl5qp5wklph5i61d96d9ifr5ijl796v1vafwrj4f3wpa")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs |