#:use-module (guix download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
+ #:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.16.0")
+ (version "1.16.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "014h2q346ynfdbpavh4p69cyv4j65hk934liq5892zznjzl73z7p"))))
+ "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.16.1")
+ (version "3.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
+ "089v16mm5m0rlyyyd0d6rz8gwb852zf3bcdrrw70wanlfjn258q7"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
("r-biocmanager" ,r-biocmanager)
- ("r-biostrings" ,r-biostrings)
- ("r-delayedarray" ,r-delayedarray)
- ("r-go-db" ,r-go-db)
("r-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
+ ("r-dbi" ,r-dbi)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-ensembldb" ,r-ensembldb)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
- ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-go-db" ,r-go-db)
+ ("r-graph" ,r-graph)
+ ("r-idr" ,r-idr)
("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-annotationdbi" ,r-annotationdbi)
("r-limma" ,r-limma)
+ ("r-matrixstats" ,r-matrixstats)
("r-multtest" ,r-multtest)
("r-rbgl" ,r-rbgl)
- ("r-graph" ,r-graph)
("r-regioner" ,r-regioner)
- ("r-dbi" ,r-dbi)
- ("r-ensembldb" ,r-ensembldb)
- ("r-biobase" ,r-biobase)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-seqinr" ,r-seqinr)
- ("r-idr" ,r-idr)
- ("r-genomicalignments" ,r-genomicalignments)
("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-rsamtools" ,r-rsamtools)
("r-venndiagram" ,r-venndiagram)))
(home-page "http://bioconductor.org/packages/ChIPpeakAnno")
(synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
(home-page "http://bioconductor.org/packages/marray")
(synopsis "Exploratory analysis for two-color spotted microarray data")
(description "This package contains class definitions for two-color spotted
-microarray data. It also includes fuctions for data input, diagnostic plots,
+microarray data. It also includes functions for data input, diagnostic plots,
normalization and quality checking.")
(license license:lgpl2.0+)))
(synopsis "Analysis of translational activity")
(description
"Genome wide studies of translational control is emerging as a tool to
-study verious biological conditions. The output from such analysis is both
+study various biological conditions. The output from such analysis is both
the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
involved in translation (the actively translating mRNA level) for each mRNA.
The standard analysis of such data strives towards identifying differential
(define-public r-rgadem
(package
(name "r-rgadem")
- (version "2.31.0")
+ (version "2.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rGADEM" version))
(sha256
(base32
- "0mck3dsxzjxszfs1cl96kd83q7n85p3763s0y3gwws69jn7p6w5j"))))
+ "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
(properties `((upstream-name . "rGADEM")))
(build-system r-build-system)
(propagated-inputs
(define-public r-ebimage
(package
(name "r-ebimage")
- (version "4.24.0")
+ (version "4.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBImage" version))
(sha256
(base32
- "18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx"))))
+ "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
(properties `((upstream-name . "EBImage")))
(build-system r-build-system)
(propagated-inputs
(define-public r-yamss
(package
(name "r-yamss")
- (version "1.8.1")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "yamss" version))
(sha256
(base32
- "13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9"))))
+ "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
(define-public r-gtrellis
(package
(name "r-gtrellis")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gtrellis" version))
(sha256
(base32
- "17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v"))))
+ "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y"))))
(build-system r-build-system)
(propagated-inputs
`(("r-circlize" ,r-circlize)
(define-public r-somaticsignatures
(package
(name "r-somaticsignatures")
- (version "2.18.0")
+ (version "2.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SomaticSignatures" version))
(sha256
(base32
- "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02"))))
+ "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
(properties
`((upstream-name . "SomaticSignatures")))
(build-system r-build-system)
(define-public r-yapsa
(package
(name "r-yapsa")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "YAPSA" version))
(sha256
(base32
- "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j"))))
+ "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
(properties `((upstream-name . "YAPSA")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gcrma
(package
(name "r-gcrma")
- (version "2.54.0")
+ (version "2.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gcrma" version))
(sha256
(base32
- "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim"))))
+ "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
(define-public r-simpleaffy
(package
(name "r-simpleaffy")
- (version "2.58.0")
+ (version "2.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "simpleaffy" version))
(sha256
(base32
- "0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s"))))
+ "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
(define-public r-yaqcaffy
(package
(name "r-yaqcaffy")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "yaqcaffy" version))
(sha256
(base32
- "192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk"))))
+ "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
(build-system r-build-system)
(propagated-inputs
`(("r-simpleaffy" ,r-simpleaffy)))
(define-public r-quantro
(package
(name "r-quantro")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "quantro" version))
(sha256
(base32
- "1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib"))))
+ "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-yarn
(package
(name "r-yarn")
- (version "1.8.1")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "yarn" version))
(sha256
(base32
- "0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s"))))
+ "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-roar
(package
(name "r-roar")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "roar" version))
(sha256
(base32
- "15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw"))))
+ "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
(define-public r-xbseq
(package
(name "r-xbseq")
- (version "1.14.1")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "XBSeq" version))
(sha256
(base32
- "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph"))))
+ "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
(properties `((upstream-name . "XBSeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-massspecwavelet
(package
(name "r-massspecwavelet")
- (version "1.48.1")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MassSpecWavelet" version))
(sha256
(base32
- "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz"))))
+ "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
(properties
`((upstream-name . "MassSpecWavelet")))
(build-system r-build-system)
(define-public r-xcms
(package
(name "r-xcms")
- (version "3.4.4")
+ (version "3.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "xcms" version))
(sha256
(base32
- "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww"))))
+ "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-wrench
(package
(name "r-wrench")
- (version "1.0.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Wrench" version))
(sha256
(base32
- "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg"))))
+ "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
(properties `((upstream-name . "Wrench")))
(build-system r-build-system)
(propagated-inputs
(define-public r-wiggleplotr
(package
(name "r-wiggleplotr")
- (version "1.6.1")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wiggleplotr" version))
(sha256
(base32
- "12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3"))))
+ "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
(define-public r-widgettools
(package
(name "r-widgettools")
- (version "1.60.0")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "widgetTools" version))
(sha256
(base32
- "0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf"))))
+ "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
(properties `((upstream-name . "widgetTools")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/widgetTools/")
(define-public r-webbioc
(package
(name "r-webbioc")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "webbioc" version))
(sha256
(base32
- "16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi"))))
+ "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
(build-system r-build-system)
(inputs
`(("netpbm" ,netpbm)
(define-public r-zfpkm
(package
(name "r-zfpkm")
- (version "1.4.1")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "zFPKM" version))
(sha256
(base32
- "0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5"))))
+ "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
(properties `((upstream-name . "zFPKM")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rbowtie2
(package
(name "r-rbowtie2")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rbowtie2" version))
(sha256
(base32
- "045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr"))))
+ "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
(properties `((upstream-name . "Rbowtie2")))
(build-system r-build-system)
(inputs
(define-public r-progeny
(package
(name "r-progeny")
- (version "1.4.1")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "progeny" version))
(sha256
(base32
- "02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7"))))
+ "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
(build-system r-build-system)
(propagated-inputs `(("r-biobase" ,r-biobase)))
(home-page "https://github.com/saezlab/progeny")
(define-public r-arrmnormalization
(package
(name "r-arrmnormalization")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ARRmNormalization" version))
(sha256
(base32
- "09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd"))))
+ "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
(properties
`((upstream-name . "ARRmNormalization")))
(build-system r-build-system)
custom Txdb objects) that are costly or difficult to create, web resources,
and data files used across sessions.")
(license license:artistic2.0)))
+
+(define-public r-iclusterplus
+ (package
+ (name "r-iclusterplus")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "iClusterPlus" version))
+ (sha256
+ (base32
+ "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
+ (properties `((upstream-name . "iClusterPlus")))
+ (build-system r-build-system)
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://bioconductor.org/packages/iClusterPlus/")
+ (synopsis "Integrative clustering of multi-type genomic data")
+ (description
+ "iClusterPlus is developed for integrative clustering analysis of
+multi-type genomic data and is an enhanced version of iCluster proposed and
+developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
+from the experiments where biological samples (e.g. tumor samples) are
+analyzed by multiple techniques, for instance, @dfn{array comparative genomic
+hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
+on. In the iClusterPlus model, binary observations such as somatic mutation
+are modeled as Binomial processes; categorical observations such as copy
+number states are realizations of Multinomial random variables; counts are
+modeled as Poisson random processes; and continuous measures are modeled by
+Gaussian distributions.")
+ (license license:gpl2+)))
+
+(define-public r-rbowtie
+ (package
+ (name "r-rbowtie")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rbowtie" version))
+ (sha256
+ (base32
+ "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
+ (properties `((upstream-name . "Rbowtie")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://bioconductor.org/packages/Rbowtie/")
+ (synopsis "R bowtie wrapper")
+ (description
+ "This package provides an R wrapper around the popular bowtie short read
+aligner and around SpliceMap, a de novo splice junction discovery and
+alignment tool.")
+ (license license:artistic2.0)))
+
+(define-public r-sgseq
+ (package
+ (name "r-sgseq")
+ (version "1.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "SGSeq" version))
+ (sha256
+ (base32
+ "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
+ (properties `((upstream-name . "SGSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-igraph" ,r-igraph)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-runit" ,r-runit)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/SGSeq/")
+ (synopsis "Splice event prediction and quantification from RNA-seq data")
+ (description
+ "SGSeq is a package for analyzing splice events from RNA-seq data. Input
+data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
+represented as a splice graph, which can be obtained from existing annotation
+or predicted from the mapped sequence reads. Splice events are identified
+from the graph and are quantified locally using structurally compatible reads
+at the start or end of each splice variant. The software includes functions
+for splice event prediction, quantification, visualization and
+interpretation.")
+ (license license:artistic2.0)))
+
+(define-public r-rhisat2
+ (package
+ (name "r-rhisat2")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhisat2" version))
+ (sha256
+ (base32
+ "01jhj5vvfl4n2d0nl3nd1iw9nii85mgw2adnrmxb8wwlxgy240vr"))))
+ (properties `((upstream-name . "Rhisat2")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("which" ,which)))
+ (propagated-inputs
+ `(("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-sgseq" ,r-sgseq)))
+ (home-page "https://github.com/fmicompbio/Rhisat2")
+ (synopsis "R Wrapper for HISAT2 sequence aligner")
+ (description
+ "This package provides an R interface to the HISAT2 spliced short-read
+aligner by Kim et al. (2015). The package contains wrapper functions to
+create a genome index and to perform the read alignment to the generated
+index.")
+ (license license:gpl3)))
+
+(define-public r-quasr
+ (package
+ (name "r-quasr")
+ (version "1.24.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "QuasR" version))
+ (sha256
+ (base32
+ "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
+ (properties `((upstream-name . "QuasR")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rbowtie" ,r-rbowtie)
+ ("r-rhisat2" ,r-rhisat2)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shortread" ,r-shortread)))
+ (home-page "https://bioconductor.org/packages/QuasR/")
+ (synopsis "Quantify and annotate short reads in R")
+ (description
+ "This package provides a framework for the quantification and analysis of
+short genomic reads. It covers a complete workflow starting from raw sequence
+reads, over creation of alignments and quality control plots, to the
+quantification of genomic regions of interest.")
+ (license license:gpl2)))
+
+(define-public r-rqc
+ (package
+ (name "r-rqc")
+ (version "1.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rqc" version))
+ (sha256
+ (base32
+ "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
+ (properties `((upstream-name . "Rqc")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biocstyle" ,r-biocstyle)
+ ("r-biostrings" ,r-biostrings)
+ ("r-biovizbase" ,r-biovizbase)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-knitr" ,r-knitr)
+ ("r-markdown" ,r-markdown)
+ ("r-plyr" ,r-plyr)
+ ("r-rcpp" ,r-rcpp)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shiny" ,r-shiny)
+ ("r-shortread" ,r-shortread)))
+ (home-page "https://github.com/labbcb/Rqc")
+ (synopsis "Quality control tool for high-throughput sequencing data")
+ (description
+ "Rqc is an optimized tool designed for quality control and assessment of
+high-throughput sequencing data. It performs parallel processing of entire
+files and produces a report which contains a set of high-resolution
+graphics.")
+ (license license:gpl2+)))
HCoop / jackhill / guix / guix.git / blobdiff