diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 138 |
1 files changed, 123 insertions, 15 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7f11dead3..20aabb0be4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2018 Roel Janssen <roel@gnu.org> +;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. @@ -197,7 +197,84 @@ default." ) genomes and gene ID formats, largely based on the UCSC table browser.") (license license:lgpl2.0+))) +(define-public r-txdb-mmusculus-ucsc-mm9-knowngene + (package + (name "r-txdb-mmusculus-ucsc-mm9-knowngene") + (version "3.2.2") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "https://bioconductor.org/packages/" + "release/data/annotation/src/contrib" + "/TxDb.Mmusculus.UCSC.mm9.knownGene_" + version ".tar.gz")) + (sha256 + (base32 + "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) + (properties + `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicfeatures" ,r-genomicfeatures) + ("r-annotationdbi" ,r-annotationdbi))) + (home-page + "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") + (synopsis "Annotation package for mouse genome in TxDb format") + (description + "This package provides an annotation database of Mouse genome data. It +is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The +database is exposed as a @code{TxDb} object.") + (license license:artistic2.0))) + +(define-public r-biocgenerics + (package + (name "r-biocgenerics") + (version "0.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocGenerics" version)) + (sha256 + (base32 + "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8")))) + (properties + `((upstream-name . "BiocGenerics"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BiocGenerics") + (synopsis "S4 generic functions for Bioconductor") + (description + "This package provides S4 generic functions needed by many Bioconductor +packages.") + (license license:artistic2.0))) + +(define-public r-annotate + (package + (name "r-annotate") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "annotate" version)) + (sha256 + (base32 + "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n")))) + (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-xml" ,r-xml) + ("r-xtable" ,r-xtable))) + (home-page + "https://bioconductor.org/packages/annotate") + (synopsis "Annotation for microarrays") + (description "This package provides R environments for the annotation of +microarrays.") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") @@ -411,14 +488,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.16.0") + (version "3.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3")))) + "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -778,14 +855,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a")))) + "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -804,14 +881,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947")))) + "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs @@ -831,14 +908,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5")))) + "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -852,33 +929,64 @@ information.") in omics data.") (license license:gpl2+))) +(define-public r-plgem + (package + (name "r-plgem") + (version "1.54.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "plgem" version)) + (sha256 + (base32 + "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-mass" ,r-mass))) + (home-page "http://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 +model the variance-versus-mean dependence that exists in a variety of +genome-wide datasets, including microarray and proteomics data. The use of +PLGEM has been shown to improve the detection of differentially expressed +genes or proteins in these datasets.") + (license license:gpl2))) + (define-public r-inspect (package (name "r-inspect") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2")))) + "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp")))) (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-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-plgem" ,r-plgem) ("r-preprocesscore" ,r-preprocesscore) ("r-proc" ,r-proc) ("r-rootsolve" ,r-rootsolve) ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-txdb-mmusculus-ucsc-mm9-knowngene" + ,r-txdb-mmusculus-ucsc-mm9-knowngene))) (home-page "https://bioconductor.org/packages/INSPEcT") (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") (description @@ -918,14 +1026,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m")))) + "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs |