X-Git-Url: https://git.hcoop.net/jackhill/guix/guix.git/blobdiff_plain/aa802eafb66fc861f70292eb6674540aeac8db1a..dddf975ffb95368b9561fe8e9ab582366dddc8f7:/gnu/packages/bioconductor.scm diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8de8d5b233..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 -;;; Copyright © 2018 Roel Janssen +;;; Copyright © 2018, 2019 Ricardo Wurmus +;;; Copyright © 2017, 2018 Roel Janssen ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; 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") @@ -219,23 +296,24 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb")))) + "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs - `(("r-memoise" ,r-memoise) - ("r-genomicranges" ,r-genomicranges) + `(("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) - ("r-rtracklayer" ,r-rtracklayer) ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-memoise" ,r-memoise) + ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") @@ -292,14 +370,14 @@ occupancy (overlap) analysis and plotting functions.") (define-public r-ripseeker (package (name "r-ripseeker") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 - "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi")))) + "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs @@ -410,14 +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 @@ -619,14 +697,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0")))) + "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -658,14 +736,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn")))) + "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -686,14 +764,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n")))) + "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -718,14 +796,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q")))) + "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -757,14 +835,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9")))) + "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") @@ -777,14 +855,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.32.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l")))) + "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -803,14 +881,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.8.2") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s")))) + "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs @@ -830,14 +908,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3")))) + "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -851,33 +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 "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p")))) + "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 @@ -890,14 +999,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0xhna7f0kr7pp2hqwara5i57m9mdr65shflfxiyw6yy3g90pgb5x")))) + "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -917,14 +1026,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.14.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj")))) + "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -939,3 +1048,131 @@ demultiplexed, i.e. assigned to their original reference barcode.") of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.") (license license:artistic2.0))) + +(define-public r-biocneighbors + (package + (name "r-biocneighbors") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocNeighbors" version)) + (sha256 + (base32 + "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll")))) + (properties `((upstream-name . "BiocNeighbors"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-rcpp" ,r-rcpp) + ("r-rcppannoy" ,r-rcppannoy) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/BiocNeighbors") + (synopsis "Nearest Neighbor Detection for Bioconductor packages") + (description + "This package implements exact and approximate methods for nearest +neighbor detection, in a framework that allows them to be easily switched +within Bioconductor packages or workflows. The exact algorithm is implemented +using pre-clustering with the k-means algorithm. Functions are also provided +to search for all neighbors within a given distance. Parallelization is +achieved for all methods using the BiocParallel framework.") + (license license:gpl3))) + +(define-public r-destiny + (package + (name "r-destiny") + (version "2.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "destiny" version)) + (sha256 + (base32 + "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-fnn" ,r-fnn) + ("r-ggthemes" ,r-ggthemes) + ("r-hmisc" ,r-hmisc) + ("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-proxy" ,r-proxy) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-scales" ,r-scales) + ("r-scatterplot3d" ,r-scatterplot3d) + ("r-smoother" ,r-smoother) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-vim" ,r-vim))) + (home-page "https://bioconductor.org/packages/destiny/") + (synopsis "Create and plot diffusion maps") + (description "This package provides tools to create and plot diffusion +maps.") + ;; Any version of the GPL + (license license:gpl3+))) + +(define-public r-savr + (package + (name "r-savr") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "savR" version)) + (sha256 + (base32 + "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7")))) + (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))) + (home-page "https://github.com/bcalder/savR") + (synopsis "Parse and analyze Illumina SAV files") + (description + "This package provides tools to parse Illumina Sequence Analysis +Viewer (SAV) files, access data, and generate QC plots.") + (license license:agpl3+))) + +(define-public r-chipexoqual + (package + (name "r-chipexoqual") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChIPexoQual" version)) + (sha256 + (base32 + "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp")))) + (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))) + (home-page "https://github.com/keleslab/ChIPexoQual") + (synopsis "Quality control pipeline for ChIP-exo/nexus data") + (description + "This package provides a quality control pipeline for ChIP-exo/nexus +sequencing data.") + (license license:gpl2+)))