diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 135 |
1 files changed, 112 insertions, 23 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c913232680..8e13044b1a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -51,6 +51,7 @@ #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages java) + #:use-module (gnu packages javascript) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) @@ -7194,13 +7195,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.36.2") + (version "1.36.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0bd46s7ch4j70n0snjf2nyx8gzkxn7d563jh5i3i0wzb647f5hbg")))) + "04bh4481jcj91xdh11ic4519jczck6zmysbpnpbbhykanp31z4pf")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7253,13 +7254,13 @@ alignments.") (define-public r-genomicdatacommons (package (name "r-genomicdatacommons") - (version "1.24.2") + (version "1.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicDataCommons" version)) (sha256 (base32 - "0dgvhi6nbc1qvrdwww2r39gxd2xmbadvy03lxh5nny9pyhhdlz3l")))) + "1grvria7lx7p0py3w8yi0j41bpfx951lds5db7jdiq0j8l75fh38")))) (properties `((upstream-name . "GenomicDataCommons"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -7272,6 +7273,7 @@ alignments.") r-readr r-rlang r-tibble + r-tidyr r-xml2)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicDataCommons") @@ -7734,6 +7736,90 @@ of other R packages who wish to make use of HTSlib.") microarray data, using nearest neighbor averaging.") (license license:gpl2+))) +(define-public r-interactivedisplay + (package + (name "r-interactivedisplay") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "interactiveDisplay" version)) + (sha256 + (base32 + "1y9fdnpz1bagrwhyj8jikp2q5fd9y74j48l5z7f0s88v88sa7szl")) + (snippet + '(for-each delete-file + '("inst/www/js/jquery.js" + "inst/www/js/jquery.min.js" + "inst/www/js/jquery.dataTables.min.js"))))) + (properties `((upstream-name . "interactiveDisplay"))) + (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) + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-jquery-1.8.2") + "inst/www/js/jquery.js") + (,(assoc-ref inputs "js-jquery-1.9.1") + "inst/www/js/jquery.min.js") + (,(search-input-file inputs + "/share/javascript/jquery.dataTables.min.js") + "inst/www/js/jquery.dataTables.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-annotationdbi + r-biocgenerics + r-biocmanager + r-category + r-dt + r-ggplot2 + r-gridsvg + r-interactivedisplaybase + r-plyr + r-rcolorbrewer + r-reshape2 + r-shiny + r-zlibbioc + r-xml)) + (native-inputs + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("js-datatables" ,js-datatables) + ("js-jquery-1.8.2" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.8.2.js") + (sha256 + (base32 + "0nikk2clbnyi02k0brvhbd8m43lfh4l1zrya35jya9sy6wb9b9ng")))) + ("js-jquery-1.9.1" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.9.1.js") + (sha256 + (base32 + "0h4dk67yc9d0kadqxb6b33585f3x3559p6qmp70l00qwq030vn3v")))))) + (home-page "https://bioconductor.org/packages/interactiveDisplay") + (synopsis "Package for Shiny web displays of Bioconductor objects") + (description + "This package offers interactive Shiny displays for Bioconductor +objects. In addition, this package empowers users to develop engaging +visualizations and interfaces for working with Bioconductor data.") + (license license:artistic2.0))) + (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") @@ -9727,13 +9813,13 @@ and advanced quality control routines.") (define-public r-shinymethyl (package (name "r-shinymethyl") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "shinyMethyl" version)) (sha256 (base32 - "1rqwwglj0475gr14bxazfmcvsy7rq6nlw2zcswa684751wy15w0r")))) + "0hq1q66vjd9pwdwm9zx8q45ws65bn6cm87zmjmyc3md8dwvb8cck")))) (properties `((upstream-name . "shinyMethyl"))) (build-system r-build-system) (propagated-inputs @@ -9877,16 +9963,17 @@ level.") (define-public r-tcgautils (package (name "r-tcgautils") - (version "1.20.2") + (version "1.20.4") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAutils" version)) (sha256 (base32 - "0nnfrd5x3mii9adizvz79jinlxn2lhg4civ9v0wwygmdhk7rrm1n")))) + "02mkijvh2h58wg7hsi76ycw6gapl0ai190agckaw4l54sqpsx91q")))) (properties `((upstream-name . "TCGAutils"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi + r-biocbaseutils r-biocgenerics r-genomeinfodb r-genomicdatacommons @@ -11023,13 +11110,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1sfpf9msnzyrc8b0xzc2406bq2gkcwrrhv7fa9ynqv2ip6xwsc8s")))) + "0z89yikglx077x18qhq6f8f2fa9xni12jz8my9p5sa6zmvnj4dnm")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs @@ -12564,14 +12651,14 @@ abnormal copy number.") (define-public r-htscluster (package (name "r-htscluster") - (version "2.0.10") + (version "2.0.11") (source (origin (method url-fetch) (uri (cran-uri "HTSCluster" version)) (sha256 (base32 - "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n")))) + "0x9shhyla9bldkkh367gfdmf0k72l1ppixb8gzsa6nf8jx8qdpbp")))) (properties `((upstream-name . "HTSCluster"))) (build-system r-build-system) (propagated-inputs @@ -14335,14 +14422,14 @@ attempts to assess their statistical significance.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.8.2") + (version "4.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "0iijby2j9i6sbdc3iwhqqb8xlz25k3dpiyq91p7yybggpr2p1nw4")))) + "1kihrpa8cb2bqk5dck0w6yzgfpl72qxlrxwpidg1ar27q3ivz8w3")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -19576,13 +19663,13 @@ routines.") (define-public r-s4arrays (package (name "r-s4arrays") - (version "1.0.5") + (version "1.0.6") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Arrays" version)) (sha256 (base32 - "01xlccybhdgas9pnx88ll9q56qb2xd687xvfrc7bd5r9sf72b81c")))) + "011n4lyznlrya5l8d7m30x81k7h81wbp07b12s6a4s5sy9fzd5jb")))) (properties `((upstream-name . "S4Arrays"))) (build-system r-build-system) (propagated-inputs @@ -19840,14 +19927,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1j8i4rmq85n7jys86a9zyj1n4qn7bhc1sqgcq8dyh7zqfdvb9bcw")) + "1007i2rzz86k04kswa4h53p8zzh52k31m9d8im6iw0n91inqbcj9")) (modules '((guix build utils))) (snippet '(begin @@ -20463,14 +20550,14 @@ Visium platform.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.22.5") + (version "1.22.6") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1bzbsfds5zki6iazj53y6kps8bvn7zdysbmpf9359sv6zshk18fv")))) + "0jaaqa2fm61dmsphm5y4rlwf2dm1l5rs0vpq0f5r35iyw2m12lh8")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -21108,14 +21195,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.7-5") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "0ibznjhy7vmh2myarvmxy06rvddbpbarbp201px62mig2pb9aq4y")))) + "100nafmyddz0c1h01fbqw5q6pji7zhg2196rkyak88za6s5ms0s4")))) (build-system r-build-system) (inputs (list gsl)) @@ -21124,11 +21211,13 @@ on the plot.") r-foreach r-graph r-lme4 + r-mclogit r-nnet r-rcpp r-rcpparmadillo r-rgraphviz - r-rjags)) + r-rjags + r-stringi)) (native-inputs (list r-r-rsp)) (home-page "https://r-bayesian-networks.org/") |