;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
#:use-module (gnu packages maths)
#:use-module (gnu packages statistics)
#:use-module (gnu packages web))
+\f
+;;; Annotations
+
+(define-public r-bsgenome-celegans-ucsc-ce6
+ (package
+ (name "r-bsgenome-celegans-ucsc-ce6")
+ (version "1.4.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Celegans.UCSC.ce6_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
+ (properties
+ `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
+ (synopsis "Full genome sequences for Worm")
+ (description
+ "This package provides full genome sequences for Caenorhabditis
+elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
+objects.")
+ (license license:artistic2.0)))
+
+(define-public r-bsgenome-celegans-ucsc-ce10
+ (package
+ (name "r-bsgenome-celegans-ucsc-ce10")
+ (version "1.4.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Celegans.UCSC.ce10_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
+ (properties
+ `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
+ (synopsis "Full genome sequences for Worm")
+ (description
+ "This package provides full genome sequences for Caenorhabditis
+elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
+objects.")
+ (license license:artistic2.0)))
+
(define-public r-bsgenome-dmelanogaster-ucsc-dm6
(package
(name "r-bsgenome-dmelanogaster-ucsc-dm6")
objects.")
(license license:artistic2.0)))
+(define-public r-bsgenome-dmelanogaster-ucsc-dm3
+ (package
+ (name "r-bsgenome-dmelanogaster-ucsc-dm3")
+ (version "1.4.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Dmelanogaster.UCSC.dm3_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
+ (properties
+ `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
+ (synopsis "Full genome sequences for Fly")
+ (description
+ "This package provides full genome sequences for Drosophila
+melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
+Biostrings objects.")
+ (license license:artistic2.0)))
+
(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
(package
(name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
(license license:artistic2.0)))
+(define-public r-bsgenome-hsapiens-1000genomes-hs37d5
+ (package
+ (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
+ (version "0.99.1")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Hsapiens.1000genomes.hs37d5_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
+ (properties
+ `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
+ (synopsis "Full genome sequences for Homo sapiens")
+ (description
+ "This package provides full genome sequences for Homo sapiens from
+1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
+ (license license:artistic2.0)))
+
(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
(package
(name "r-bsgenome-hsapiens-ucsc-hg19-masked")
default.")
(license license:artistic2.0)))
+(define-public r-bsgenome-mmusculus-ucsc-mm9
+ (package
+ (name "r-bsgenome-mmusculus-ucsc-mm9")
+ (version "1.4.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Mmusculus.UCSC.mm9_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
+ (properties
+ `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
+ (synopsis "Full genome sequences for Mouse")
+ (description
+ "This package provides full genome sequences for Mus musculus (Mouse) as
+provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
+ (license license:artistic2.0)))
+
(define-public r-bsgenome-mmusculus-ucsc-mm9-masked
(package
(name "r-bsgenome-mmusculus-ucsc-mm9-masked")
default." )
(license license:artistic2.0)))
-(define-public r-genelendatabase
+(define-public r-bsgenome-mmusculus-ucsc-mm10
+ (package
+ (name "r-bsgenome-mmusculus-ucsc-mm10")
+ (version "1.4.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Mmusculus.UCSC.mm10_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
+ (properties
+ `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
+ (synopsis "Full genome sequences for Mouse")
+ (description
+ "This package provides full genome sequences for Mus
+musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
+in Biostrings objects.")
+ (license license:artistic2.0)))
+
+(define-public r-org-ce-eg-db
+ (package
+ (name "r-org-ce-eg-db")
+ (version "3.7.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "org.Ce.eg.db_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
+ (properties
+ `((upstream-name . "org.Ce.eg.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
+ (synopsis "Genome wide annotation for Worm")
+ (description
+ "This package provides mappings from Entrez gene identifiers to various
+annotations for the genome of the model worm Caenorhabditis elegans.")
+ (license license:artistic2.0)))
+
+(define-public r-org-dm-eg-db
+ (package
+ (name "r-org-dm-eg-db")
+ (version "3.7.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "org.Dm.eg.db_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
+ (properties
+ `((upstream-name . "org.Dm.eg.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
+ (synopsis "Genome wide annotation for Fly")
+ (description
+ "This package provides mappings from Entrez gene identifiers to various
+annotations for the genome of the model fruit fly Drosophila melanogaster.")
+ (license license:artistic2.0)))
+
+(define-public r-org-dr-eg-db
+ (package
+ (name "r-org-dr-eg-db")
+ (version "3.7.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "org.Dr.eg.db_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
+ (properties
+ `((upstream-name . "org.Dr.eg.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
+ (synopsis "Annotation for Zebrafish")
+ (description
+ "This package provides genome wide annotations for Zebrafish, primarily
+based on mapping using Entrez Gene identifiers.")
+ (license license:artistic2.0)))
+
+(define-public r-org-hs-eg-db
+ (package
+ (name "r-org-hs-eg-db")
+ (version "3.7.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "org.Hs.eg.db_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
+ (properties
+ `((upstream-name . "org.Hs.eg.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
+ (synopsis "Genome wide annotation for Human")
+ (description
+ "This package contains genome-wide annotations for Human, primarily based
+on mapping using Entrez Gene identifiers.")
+ (license license:artistic2.0)))
+
+(define-public r-org-mm-eg-db
+ (package
+ (name "r-org-mm-eg-db")
+ (version "3.7.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "org.Mm.eg.db_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
+ (properties
+ `((upstream-name . "org.Mm.eg.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
+ (synopsis "Genome wide annotation for Mouse")
+ (description
+ "This package provides mappings from Entrez gene identifiers to various
+annotations for the genome of the model mouse Mus musculus.")
+ (license license:artistic2.0)))
+
+(define-public r-bsgenome-hsapiens-ucsc-hg19
+ (package
+ (name "r-bsgenome-hsapiens-ucsc-hg19")
+ (version "1.4.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Hsapiens.UCSC.hg19_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
+ (properties
+ `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
+ (synopsis "Full genome sequences for Homo sapiens")
+ (description
+ "This package provides full genome sequences for Homo sapiens as provided
+by UCSC (hg19, February 2009) and stored in Biostrings objects.")
+ (license license:artistic2.0)))
+
+(define-public r-genelendatabase
+ (package
+ (name "r-genelendatabase")
+ (version "1.18.0")
+ (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
+ "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
+ (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-hsapiens-ucsc-hg19-knowngene
+ (package
+ (name "r-txdb-hsapiens-ucsc-hg19-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.Hsapiens.UCSC.hg19.knownGene_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
+ (properties
+ `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-genomicfeatures" ,r-genomicfeatures)))
+ (home-page
+ "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
+ (synopsis "Annotation package for human genome in TxDb format")
+ (description
+ "This package provides an annotation database of Homo sapiens genome
+data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
+track. The database is exposed as a @code{TxDb} object.")
+ (license license:artistic2.0)))
+
+(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-txdb-mmusculus-ucsc-mm10-knowngene
+ (package
+ (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
+ (version "3.4.4")
+ (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://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "TxDb.Mmusculus.UCSC.mm10.knownGene_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
+ (properties
+ `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-annotationdbi" ,r-annotationdbi)))
+ (home-page
+ "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
+ (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
+ (description
+ "This package loads a TxDb object, which is an R interface to
+prefabricated databases contained in this package. This package provides
+the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
+based on the knownGene track.")
+ (license license:artistic2.0)))
+
+\f
+;;; Experiment data
+
+(define-public r-hsmmsinglecell
+ (package
+ (name "r-hsmmsinglecell")
+ (version "1.2.0")
+ (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://www.bioconductor.org/packages/"
+ "release/data/experiment/src/contrib/"
+ "HSMMSingleCell_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
+ (properties
+ `((upstream-name . "HSMMSingleCell")))
+ (build-system r-build-system)
+ (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
+ (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
+ (description
+ "Skeletal myoblasts undergo a well-characterized sequence of
+morphological and transcriptional changes during differentiation. In this
+experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
+under high mitogen conditions (GM) and then differentiated by switching to
+low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
+hundred cells taken over a time-course of serum-induced differentiation.
+Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
+72 hours) following serum switch using the Fluidigm C1 microfluidic system.
+RNA from each cell was isolated and used to construct mRNA-Seq libraries,
+which were then sequenced to a depth of ~4 million reads per library,
+resulting in a complete gene expression profile for each cell.")
+ (license license:artistic2.0)))
+
+\f
+;;; Packages
+
+(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-genelendatabase")
- (version "1.16.0")
+ (name "r-annotate")
+ (version "1.60.0")
(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"))
+ (uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5"))))
- (properties
- `((upstream-name . "geneLenDataBase")))
+ "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
(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+)))
+ `(("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)))
-\f
(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")
region sets and other genomic features.")
(license license:artistic2.0)))
+(define-public r-geneplotter
+ (package
+ (name "r-geneplotter")
+ (version "1.60.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "geneplotter" version))
+ (sha256
+ (base32
+ "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-lattice" ,r-lattice)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "https://bioconductor.org/packages/geneplotter")
+ (synopsis "Graphics functions for genomic data")
+ (description
+ "This package provides functions for plotting genomic data.")
+ (license license:artistic2.0)))
+
+(define-public r-qvalue
+ (package
+ (name "r-qvalue")
+ (version "2.14.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "qvalue" version))
+ (sha256
+ (base32
+ "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-reshape2" ,r-reshape2)))
+ (home-page "http://github.com/jdstorey/qvalue")
+ (synopsis "Q-value estimation for false discovery rate control")
+ (description
+ "This package takes a list of p-values resulting from the simultaneous
+testing of many hypotheses and estimates their q-values and local @dfn{false
+discovery rate} (FDR) values. The q-value of a test measures the proportion
+of false positives incurred when that particular test is called significant.
+The local FDR measures the posterior probability the null hypothesis is true
+given the test's p-value. Various plots are automatically generated, allowing
+one to make sensible significance cut-offs. The software can be applied to
+problems in genomics, brain imaging, astrophysics, and data mining.")
+ ;; Any version of the LGPL.
+ (license license:lgpl3+)))
+
(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 "1.58.0")
+ (version "1.60.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
- (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
+ (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
(build-system r-build-system)
(propagated-inputs
`(("r-limma" ,r-limma)))
(define-public r-cghbase
(package
(name "r-cghbase")
- (version "1.40.0")
+ (version "1.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
- (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
+ (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
(define-public r-cghcall
(package
(name "r-cghcall")
- (version "2.42.0")
+ (version "2.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
- (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
+ (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
- (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
+ (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-bayseq
(package
(name "r-bayseq")
- (version "2.14.0")
+ (version "2.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "baySeq" version))
(sha256
(base32
- "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
+ "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
(properties `((upstream-name . "baySeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-chipcomp
(package
(name "r-chipcomp")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPComp" version))
(sha256
(base32
- "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
+ "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
(properties `((upstream-name . "ChIPComp")))
(build-system r-build-system)
(propagated-inputs
(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
(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
(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)
(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)
(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/")
(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)
(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
(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
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
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+)))
+
+(define-public r-copynumber
+ (package
+ (name "r-copynumber")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "copynumber" version))
+ (sha256
+ (base32
+ "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-s4vectors" ,r-s4vectors)
+ ("r-iranges" ,r-iranges)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-biocgenerics" ,r-biocgenerics)))
+ (home-page "https://bioconductor.org/packages/copynumber")
+ (synopsis "Segmentation of single- and multi-track copy number data")
+ (description
+ "This package segments single- and multi-track copy number data by a
+penalized least squares regression method.")
+ (license license:artistic2.0)))
+
+(define-public r-dnacopy
+ (package
+ (name "r-dnacopy")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DNAcopy" version))
+ (sha256
+ (base32
+ "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
+ (properties `((upstream-name . "DNAcopy")))
+ (build-system r-build-system)
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://bioconductor.org/packages/DNAcopy")
+ (synopsis "DNA copy number data analysis")
+ (description
+ "This package implements the @dfn{circular binary segmentation} (CBS)
+algorithm to segment DNA copy number data and identify genomic regions with
+abnormal copy number.")
+ (license license:gpl2+)))
+
+;; This is a CRAN package, but it uncharacteristically depends on a
+;; Bioconductor package.
+(define-public r-htscluster
+ (package
+ (name "r-htscluster")
+ (version "2.0.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "HTSCluster" version))
+ (sha256
+ (base32
+ "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
+ (properties `((upstream-name . "HTSCluster")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-capushe" ,r-capushe)
+ ("r-edger" ,r-edger)
+ ("r-plotrix" ,r-plotrix)))
+ (home-page "https://cran.r-project.org/web/packages/HTSCluster")
+ (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
+ (description
+ "This package provides a Poisson mixture model is implemented to cluster
+genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
+estimation is performed using either the EM or CEM algorithm, and the slope
+heuristics are used for model selection (i.e., to choose the number of
+clusters).")
+ (license license:gpl3+)))
+
+(define-public r-deds
+ (package
+ (name "r-deds")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DEDS" version))
+ (sha256
+ (base32
+ "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
+ (properties `((upstream-name . "DEDS")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/DEDS/")
+ (synopsis "Differential expression via distance summary for microarray data")
+ (description
+ "This library contains functions that calculate various statistics of
+differential expression for microarray data, including t statistics, fold
+change, F statistics, SAM, moderated t and F statistics and B statistics. It
+also implements a new methodology called DEDS (Differential Expression via
+Distance Summary), which selects differentially expressed genes by integrating
+and summarizing a set of statistics using a weighted distance approach.")
+ ;; Any version of the LGPL.
+ (license license:lgpl3+)))
+
+;; This is a CRAN package, but since it depends on a Bioconductor package we
+;; put it here.
+(define-public r-nbpseq
+ (package
+ (name "r-nbpseq")
+ (version "0.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "NBPSeq" version))
+ (sha256
+ (base32
+ "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
+ (properties `((upstream-name . "NBPSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-qvalue" ,r-qvalue)))
+ (home-page "https://cran.r-project.org/web/packages/NBPSeq")
+ (synopsis "Negative binomial models for RNA-Seq data")
+ (description
+ "This package provides negative binomial models for two-group comparisons
+and regression inferences from RNA-sequencing data.")
+ (license license:gpl2)))
HCoop / jackhill / guix / guix.git / blobdiff