;;; 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.
#:use-module (guix download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
+ #:use-module (gnu packages bioinformatics)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages graph)
+ #:use-module (gnu packages maths)
#:use-module (gnu packages statistics)
- #:use-module (gnu packages bioinformatics))
+ #:use-module (gnu packages web))
(define-public r-bsgenome-dmelanogaster-ucsc-dm6
(package
objects.")
(license license:artistic2.0)))
+(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
+ (package
+ (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
+ (version "1.3.99")
+ (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 "http://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
+ (properties
+ `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-dmelanogaster-ucsc-dm3"
+ ,r-bsgenome-dmelanogaster-ucsc-dm3)))
+ (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
+ (synopsis "Full masked genome sequences for Fly")
+ (description
+ "This package provides full masked genome sequences for Drosophila
+melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
+Biostrings objects. The sequences are the same as in
+BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
+masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
+intra-contig ambiguities (AMB mask), (3) the mask of repeats from
+RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
+Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
+ (license license:artistic2.0)))
+
+(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
+ (package
+ (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
+ (version "1.3.99")
+ (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 "http://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Hsapiens.UCSC.hg19.masked_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
+ (properties
+ `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-hsapiens-ucsc-hg19"
+ ,r-bsgenome-hsapiens-ucsc-hg19)))
+ (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
+ (synopsis "Full masked genome sequences for Homo sapiens")
+ (description
+ "This package provides full genome sequences for Homo sapiens (Human) as
+provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
+sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
+them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
+mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
+repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
+Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
+default.")
+ (license license:artistic2.0)))
+
+(define-public r-bsgenome-mmusculus-ucsc-mm9-masked
+ (package
+ (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
+ (version "1.3.99")
+ (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 "http://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Mmusculus.UCSC.mm9.masked_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
+ (properties
+ `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-mmusculus-ucsc-mm9"
+ ,r-bsgenome-mmusculus-ucsc-mm9)))
+ (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
+ (synopsis "Full masked genome sequences for Mouse")
+ (description
+ "This package provides full genome sequences for Mus musculus (Mouse) as
+provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
+sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
+them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
+mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
+repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
+Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
+default." )
+ (license license:artistic2.0)))
+
+(define-public r-genelendatabase
+ (package
+ (name "r-genelendatabase")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/experiment/" instead of "bioc/".
+ (uri (string-append "https://bioconductor.org/packages/"
+ "release/data/experiment/src/contrib"
+ "/geneLenDataBase_" version ".tar.gz"))
+ (sha256
+ (base32
+ "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5"))))
+ (properties
+ `((upstream-name . "geneLenDataBase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rtracklayer" ,r-rtracklayer)
+ ("r-genomicfeatures" ,r-genomicfeatures)))
+ (home-page "https://bioconductor.org/packages/geneLenDataBase/")
+ (synopsis "Lengths of mRNA transcripts for a number of genomes")
+ (description
+ "This package provides the lengths of mRNA transcripts for a number of
+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")
- (version "1.22.2")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hpar" version))
(sha256
(base32
- "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
+ "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/hpar/")
(synopsis "Human Protein Atlas in R")
(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-diffbind
(package
(name "r-diffbind")
- (version "2.8.0")
+ (version "2.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
- "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
+ "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(inputs
(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
(define-public r-multtest
(package
(name "r-multtest")
- (version "2.36.0")
+ (version "2.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "multtest" version))
(sha256
(base32
- "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
+ "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-survival" ,r-survival)
expressed genes in DNA microarray experiments.")
(license license:lgpl3)))
+(define-public r-graph
+ (package
+ (name "r-graph")
+ (version "1.60.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "graph" version))
+ (sha256
+ (base32
+ "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)))
+ (home-page "https://bioconductor.org/packages/graph")
+ (synopsis "Handle graph data structures in R")
+ (description
+ "This package implements some simple graph handling capabilities for R.")
+ (license license:artistic2.0)))
+
+(define-public r-codedepends
+ (package
+ (name "r-codedepends")
+ (version "0.6.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "CodeDepends" version))
+ (sha256
+ (base32
+ "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
+ (properties `((upstream-name . "CodeDepends")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-codetools" ,r-codetools)
+ ("r-graph" ,r-graph)
+ ("r-xml" ,r-xml)))
+ (home-page "http://cran.r-project.org/web/packages/CodeDepends")
+ (synopsis "Analysis of R code for reproducible research and code comprehension")
+ (description
+ "This package provides tools for analyzing R expressions or blocks of
+code and determining the dependencies between them. It focuses on R scripts,
+but can be used on the bodies of functions. There are many facilities
+including the ability to summarize or get a high-level view of code,
+determining dependencies between variables, code improvement suggestions.")
+ ;; Any version of the GPL
+ (license (list license:gpl2+ license:gpl3+))))
+
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.14.0")
+ (version "3.16.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0"))))
+ "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
("r-biostrings" ,r-biostrings)
("r-delayedarray" ,r-delayedarray)
("r-go-db" ,r-go-db)
("r-multtest" ,r-multtest)
("r-rbgl" ,r-rbgl)
("r-graph" ,r-graph)
- ("r-biocinstaller" ,r-biocinstaller)
("r-regioner" ,r-regioner)
("r-dbi" ,r-dbi)
("r-ensembldb" ,r-ensembldb)
(define-public r-marray
(package
(name "r-marray")
- (version "1.56.0")
+ (version "1.60.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
- (base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic"))))
+ (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-limma" ,r-limma)))
+ `(("r-limma" ,r-limma)))
(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
(define-public r-cghbase
(package
(name "r-cghbase")
- (version "1.38.0")
+ (version "1.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
- (base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm"))))
+ (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
(define-public r-cghcall
(package
(name "r-cghcall")
- (version "2.40.0")
+ (version "2.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
- (base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch"))))
+ (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
- (version "1.14.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
- (base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy"))))
+ (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
+ ("r-biocparallel" ,r-biocparallel)
("r-cghbase" ,r-cghbase)
("r-cghcall" ,r-cghcall)
("r-dnacopy" ,r-dnacopy)
segmentation and calling are also implemented via packages DNAcopy and CGHcall,
respectively.")
(license license:gpl2+)))
+
+(define-public r-bayseq
+ (package
+ (name "r-bayseq")
+ (version "2.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "baySeq" version))
+ (sha256
+ (base32
+ "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
+ (properties `((upstream-name . "baySeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-abind" ,r-abind)
+ ("r-edger" ,r-edger)
+ ("r-genomicranges" ,r-genomicranges)))
+ (home-page "https://bioconductor.org/packages/baySeq/")
+ (synopsis "Bayesian analysis of differential expression patterns in count data")
+ (description
+ "This package identifies differential expression in high-throughput count
+data, such as that derived from next-generation sequencing machines,
+calculating estimated posterior likelihoods of differential expression (or
+more complex hypotheses) via empirical Bayesian methods.")
+ (license license:gpl3)))
+
+(define-public r-chipcomp
+ (package
+ (name "r-chipcomp")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ChIPComp" version))
+ (sha256
+ (base32
+ "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
+ (properties `((upstream-name . "ChIPComp")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+ ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-limma" ,r-limma)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/ChIPComp")
+ (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
+ (description
+ "ChIPComp implements a statistical method for quantitative comparison of
+multiple ChIP-seq datasets. It detects differentially bound sharp binding
+sites across multiple conditions considering matching control in ChIP-seq
+datasets.")
+ ;; Any version of the GPL.
+ (license license:gpl3+)))
+
+(define-public r-riboprofiling
+ (package
+ (name "r-riboprofiling")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RiboProfiling" version))
+ (sha256
+ (base32
+ "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
+ (properties `((upstream-name . "RiboProfiling")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-data-table" ,r-data-table)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbio" ,r-ggbio)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-plyr" ,r-plyr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-sqldf" ,r-sqldf)))
+ (home-page "https://bioconductor.org/packages/RiboProfiling/")
+ (synopsis "Ribosome profiling data analysis")
+ (description "Starting with a BAM file, this package provides the
+necessary functions for quality assessment, read start position recalibration,
+the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
+of count data: pairs, log fold-change, codon frequency and coverage
+assessment, principal component analysis on codon coverage.")
+ (license license:gpl3)))
+
+(define-public r-riboseqr
+ (package
+ (name "r-riboseqr")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "riboSeqR" version))
+ (sha256
+ (base32
+ "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
+ (properties `((upstream-name . "riboSeqR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-abind" ,r-abind)
+ ("r-bayseq" ,r-bayseq)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-seqlogo" ,r-seqlogo)))
+ (home-page "https://bioconductor.org/packages/riboSeqR/")
+ (synopsis "Analysis of sequencing data from ribosome profiling experiments")
+ (description
+ "This package provides plotting functions, frameshift detection and
+parsing of genetic sequencing data from ribosome profiling experiments.")
+ (license license:gpl3)))
+
+(define-public r-interactionset
+ (package
+ (name "r-interactionset")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "InteractionSet" version))
+ (sha256
+ (base32
+ "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
+ (properties
+ `((upstream-name . "InteractionSet")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/InteractionSet")
+ (synopsis "Base classes for storing genomic interaction data")
+ (description
+ "This packages provides the @code{GInteractions},
+@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
+for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
+experiments.")
+ (license license:gpl3)))
+
+(define-public r-genomicinteractions
+ (package
+ (name "r-genomicinteractions")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicInteractions" version))
+ (sha256
+ (base32
+ "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
+ (properties
+ `((upstream-name . "GenomicInteractions")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gviz" ,r-gviz)
+ ("r-igraph" ,r-igraph)
+ ("r-interactionset" ,r-interactionset)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-stringr" ,r-stringr)))
+ (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
+ (synopsis "R package for handling genomic interaction data")
+ (description
+ "This R package provides tools for handling genomic interaction data,
+such as ChIA-PET/Hi-C, annotating genomic features with interaction
+information and producing various plots and statistics.")
+ (license license:gpl3)))
+
+(define-public r-ctc
+ (package
+ (name "r-ctc")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ctc" version))
+ (sha256
+ (base32
+ "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-amap" ,r-amap)))
+ (home-page "https://bioconductor.org/packages/ctc/")
+ (synopsis "Cluster and tree conversion")
+ (description
+ "This package provides tools for exporting and importing classification
+trees and clusters to other programs.")
+ (license license:gpl2)))
+
+(define-public r-goseq
+ (package
+ (name "r-goseq")
+ (version "1.34.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "goseq" version))
+ (sha256
+ (base32
+ "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biasedurn" ,r-biasedurn)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genelendatabase" ,r-genelendatabase)
+ ("r-go-db" ,r-go-db)
+ ("r-mgcv" ,r-mgcv)))
+ (home-page "https://bioconductor.org/packages/goseq/")
+ (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
+ (description
+ "This package provides tools to detect Gene Ontology and/or other user
+defined categories which are over/under represented in RNA-seq data.")
+ (license license:lgpl2.0+)))
+
+(define-public r-glimma
+ (package
+ (name "r-glimma")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Glimma" version))
+ (sha256
+ (base32
+ "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
+ (properties `((upstream-name . "Glimma")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-edger" ,r-edger)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/Shians/Glimma")
+ (synopsis "Interactive HTML graphics")
+ (description
+ "This package generates interactive visualisations for analysis of
+RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
+HTML page. The interactions are built on top of the popular static
+representations of analysis results in order to provide additional
+information.")
+ (license license:lgpl3)))
+
+(define-public r-rots
+ (package
+ (name "r-rots")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ROTS" version))
+ (sha256
+ (base32
+ "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
+ (properties `((upstream-name . "ROTS")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://bioconductor.org/packages/ROTS/")
+ (synopsis "Reproducibility-Optimized Test Statistic")
+ (description
+ "This package provides tools for calculating the
+@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
+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 "1.12.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "INSPEcT" version))
+ (sha256
+ (base32
+ "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-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
+ "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
+Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
+order to evaluate synthesis, processing and degradation rates and assess via
+modeling the rates that determines changes in mature mRNA levels.")
+ (license license:gpl2)))
+
+(define-public r-dnabarcodes
+ (package
+ (name "r-dnabarcodes")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DNABarcodes" version))
+ (sha256
+ (base32
+ "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
+ (properties `((upstream-name . "DNABarcodes")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://bioconductor.org/packages/DNABarcodes")
+ (synopsis "Create and analyze DNA barcodes")
+ (description
+ "This package offers tools to create DNA barcode sets capable of
+correcting insertion, deletion, and substitution errors. Existing barcodes
+can be analyzed regarding their minimal, maximal and average distances between
+barcodes. Finally, reads that start with a (possibly mutated) barcode can be
+demultiplexed, i.e. assigned to their original reference barcode.")
+ (license license:gpl2)))
+
+(define-public r-ruvseq
+ (package
+ (name "r-ruvseq")
+ (version "1.16.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RUVSeq" version))
+ (sha256
+ (base32
+ "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
+ (properties `((upstream-name . "RUVSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-edaseq" ,r-edaseq)
+ ("r-edger" ,r-edger)
+ ("r-mass" ,r-mass)))
+ (home-page "https://github.com/drisso/RUVSeq")
+ (synopsis "Remove unwanted variation from RNA-Seq data")
+ (description
+ "This package implements methods to @dfn{remove unwanted variation} (RUV)
+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+)))