;;; 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.
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)))
+
\f
+(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")
(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")
(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
(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)
(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
(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
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
(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
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+)))
HCoop / jackhill / guix / guix.git / blobdiff