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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages bioconductor)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-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)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages image)
#:use-module (gnu packages maths)
#:use-module (gnu packages netpbm)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (srfi srfi-1))
;;; Annotations
(define-public r-reactome-db
(package
(name "r-reactome-db")
(version "1.70.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "reactome.db" version 'annotation))
(sha256
(base32
"05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
(properties `((upstream-name . "reactome.db")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)))
(home-page "https://bioconductor.org/packages/reactome.db/")
(synopsis "Annotation maps for reactome")
(description
"This package provides a set of annotation maps for the REACTOME
database, assembled using data from REACTOME.")
(license license:cc-by4.0)))
(define-public r-bsgenome-celegans-ucsc-ce6
(package
(name "r-bsgenome-celegans-ucsc-ce6")
(version "1.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
version 'annotation))
(sha256
(base32
"0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
(properties
`((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
(build-system r-build-system)
(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)
(uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
version 'annotation))
(sha256
(base32
"1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
(properties
`((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
(build-system r-build-system)
(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")
(version "1.4.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
version 'annotation))
(sha256
(base32
"1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
(properties
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
(build-system r-build-system)
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
(synopsis "Full genome sequences for Fly")
(description
"This package provides full genome sequences for Drosophila
melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
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)
(uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
version 'annotation))
(sha256
(base32
"19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
(properties
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
(build-system r-build-system)
(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")
(version "1.3.99")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
version 'annotation))
(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-1000genomes-hs37d5
(package
(name "r-bsgenome-hsapiens-1000genomes-hs37d5")
(version "0.99.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
version 'annotation))
(sha256
(base32
"1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
(properties
`((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
(build-system r-build-system)
(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-ncbi-grch38
(package
(name "r-bsgenome-hsapiens-ncbi-grch38")
(version "1.3.1000")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
version 'annotation))
(sha256
(base32
"0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
(properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
(build-system r-build-system)
(propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
(home-page
"https://bioconductor.org/packages/release/data/annotation/html/\
BSgenome.Hsapiens.NCBI.GRCh38.html")
(synopsis "Full genome sequences for Homo sapiens (GRCh38)")
(description
"This package provides full genome sequences for Homo sapiens (Human) as
provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
(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)
(uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
version 'annotation))
(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
(package
(name "r-bsgenome-mmusculus-ucsc-mm9")
(version "1.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
version 'annotation))
(sha256
(base32
"1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
(properties
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
(build-system r-build-system)
(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")
(version "1.3.99")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
version 'annotation))
(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 "https://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-bsgenome-mmusculus-ucsc-mm10
(package
(name "r-bsgenome-mmusculus-ucsc-mm10")
(version "1.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
version 'annotation))
(sha256
(base32
"12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
(properties
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
(build-system r-build-system)
(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)
(uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
(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)
(uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
(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)
(uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
(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)
(uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
(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)
(uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
(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)
(uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
version 'annotation))
(sha256
(base32
"1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
(properties
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
(build-system r-build-system)
(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-bsgenome-hsapiens-ucsc-hg38
(package
(name "r-bsgenome-hsapiens-ucsc-hg38")
(version "1.4.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
version 'annotation))
(sha256
(base32
"1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
(properties
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
(build-system r-build-system)
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
(synopsis "Full genome sequences for Homo sapiens")
(description
"This package provides full genome sequences for Homo sapiens (Human)
as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
(license license:artistic2.0)))
(define-public r-ensdb-hsapiens-v75
(package
(name "r-ensdb-hsapiens-v75")
(version "2.99.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
(sha256
(base32
"0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
(properties
`((upstream-name . "EnsDb.Hsapiens.v75")))
(build-system r-build-system)
(propagated-inputs
`(("r-ensembldb" ,r-ensembldb)))
(home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
(synopsis "Ensembl based annotation package")
(description
"This package exposes an annotation database generated from Ensembl.")
(license license:artistic2.0)))
(define-public r-genelendatabase
(package
(name "r-genelendatabase")
(version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geneLenDataBase" version 'experiment))
(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)
(uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
version 'annotation))
(sha256
(base32
"1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
(properties
`((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
(build-system r-build-system)
(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-hsapiens-ucsc-hg38-knowngene
(package
(name "r-txdb-hsapiens-ucsc-hg38-knowngene")
(version "3.4.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
version 'annotation))
(sha256
(base32
"12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
(properties
`((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
(build-system r-build-system)
(propagated-inputs
`(("r-genomicfeatures" ,r-genomicfeatures)))
(home-page
"https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.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 hg38 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)
(uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
version 'annotation))
(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 "3.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
version 'annotation))
(sha256
(base32
"0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
(properties
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(build-system r-build-system)
(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)))
(define-public r-txdb-celegans-ucsc-ce6-ensgene
(package
(name "r-txdb-celegans-ucsc-ce6-ensgene")
(version "3.2.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
version 'annotation))
(sha256
(base32
"1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
(properties
`((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-genomicfeatures" ,r-genomicfeatures)))
(home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
(synopsis "Annotation package for C elegans TxDb objects")
(description
"This package exposes a C elegans annotation database generated from UCSC
by exposing these as TxDb objects.")
(license license:artistic2.0)))
(define-public r-fdb-infiniummethylation-hg19
(package
(name "r-fdb-infiniummethylation-hg19")
(version "2.2.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
version 'annotation))
(sha256
(base32
"0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
(properties
`((upstream-name . "FDb.InfiniumMethylation.hg19")))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
("r-genomicfeatures" ,r-genomicfeatures)
("r-annotationdbi" ,r-annotationdbi)
("r-org-hs-eg-db" ,r-org-hs-eg-db)
("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
(home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
(synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
(description
"This is an annotation package for Illumina Infinium DNA methylation
probes. It contains the compiled HumanMethylation27 and HumanMethylation450
annotations.")
(license license:artistic2.0)))
(define-public r-illuminahumanmethylationepicmanifest
(package
(name "r-illuminahumanmethylationepicmanifest")
(version "0.3.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
version 'annotation))
(sha256
(base32
"0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
(properties
`((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
(build-system r-build-system)
(propagated-inputs
`(("r-minfi" ,r-minfi)))
(home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
(synopsis "Manifest for Illumina's EPIC methylation arrays")
(description
"This is a manifest package for Illumina's EPIC methylation arrays.")
(license license:artistic2.0)))
(define-public r-ideoviz
(package
(name "r-ideoviz")
(version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IdeoViz" version))
(sha256
(base32
"0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-iranges" ,r-iranges)
("r-genomicranges" ,r-genomicranges)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rtracklayer" ,r-rtracklayer)
("r-genomeinfodb" ,r-genomeinfodb)))
(home-page "https://bioconductor.org/packages/IdeoViz/")
(synopsis "Plots data along a chromosomal ideogram")
(description "This package provides functions to plot data associated with
arbitrary genomic intervals along chromosomal ideogram.")
(license license:gpl2)))
;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
;; from Bioconductor.
(define-public r-deconstructsigs
(package
(name "r-deconstructsigs")
(version "1.8.0")
(source (origin
(method url-fetch)
(uri (cran-uri "deconstructSigs" version))
(sha256
(base32
"014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
(properties
`((upstream-name . "deconstructSigs")))
(build-system r-build-system)
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)
("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
("r-genomeinfodb" ,r-genomeinfodb)
("r-reshape2" ,r-reshape2)))
(home-page "https://github.com/raerose01/deconstructSigs")
(synopsis "Identifies signatures present in a tumor sample")
(description "This package takes sample information in the form of the
fraction of mutations in each of 96 trinucleotide contexts and identifies
the weighted combination of published signatures that, when summed, most
closely reconstructs the mutational profile.")
(license license:gpl2+)))
;; This is a CRAN package, but it depends on Bioconductor packages.
(define-public r-nmf
(package
(name "r-nmf")
(version "0.22.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "NMF" version))
(sha256
(base32
"0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq"))))
(properties `((upstream-name . "NMF")))
(build-system r-build-system)
(propagated-inputs
`(("r-cluster" ,r-cluster)
("r-biobase" ,r-biobase)
("r-biocmanager" ,r-biocmanager)
("r-bigmemory" ,r-bigmemory) ; suggested
("r-synchronicity" ,r-synchronicity) ; suggested
("r-colorspace" ,r-colorspace)
("r-digest" ,r-digest)
("r-doparallel" ,r-doparallel)
("r-foreach" ,r-foreach)
("r-ggplot2" ,r-ggplot2)
("r-gridbase" ,r-gridbase)
("r-pkgmaker" ,r-pkgmaker)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-registry" ,r-registry)
("r-reshape2" ,r-reshape2)
("r-rngtools" ,r-rngtools)
("r-stringr" ,r-stringr)))
(home-page "http://renozao.github.io/NMF")
(synopsis "Algorithms and framework for nonnegative matrix factorization")
(description
"This package provides a framework to perform Non-negative Matrix
Factorization (NMF). The package implements a set of already published
algorithms and seeding methods, and provides a framework to test, develop and
plug new or custom algorithms. Most of the built-in algorithms have been
optimized in C++, and the main interface function provides an easy way of
performing parallel computations on multicore machines.")
(license license:gpl2+)))
(define-public r-do-db
(package
(name "r-do-db")
(version "2.9")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DO.db" version 'annotation))
(sha256
(base32
"10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
(properties
`((upstream-name . "DO.db")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)))
(home-page "https://www.bioconductor.org/packages/DO.db/")
(synopsis "Annotation maps describing the entire Disease Ontology")
(description
"This package provides a set of annotation maps describing the entire
Disease Ontology.")
(license license:artistic2.0)))
(define-public r-pasilla
(package
(name "r-pasilla")
(version "1.14.0")
(source (origin
(method url-fetch)
(uri (string-append
"http://bioconductor.org/packages/release/data/experiment"
"/src/contrib/pasilla_" version ".tar.gz"))
(sha256
(base32
"0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocstyle" ,r-biocstyle)
("r-dexseq" ,r-dexseq)
("r-knitr" ,r-knitr)
("r-rmarkdown" ,r-rmarkdown)))
(home-page "https://www.bioconductor.org/packages/pasilla/")
(synopsis "Data package with per-exon and per-gene read counts")
(description "This package provides per-exon and per-gene read counts
computed for selected genes from RNA-seq data that were presented in the
article 'Conservation of an RNA regulatory map between Drosophila and mammals'
by Brooks et al., Genome Research 2011.")
(license license:lgpl2.1+)))
(define-public r-pfam-db
(package
(name "r-pfam-db")
(version "3.8.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "PFAM.db" version 'annotation))
(sha256
(base32
"0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
(properties `((upstream-name . "PFAM.db")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)))
(home-page "https://bioconductor.org/packages/PFAM.db")
(synopsis "Set of protein ID mappings for PFAM")
(description
"This package provides a set of protein ID mappings for PFAM, assembled
using data from public repositories.")
(license license:artistic2.0)))
(define-public r-phastcons100way-ucsc-hg19
(package
(name "r-phastcons100way-ucsc-hg19")
(version "3.7.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "phastCons100way.UCSC.hg19"
version 'annotation))
(sha256
(base32
"1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
(properties
`((upstream-name . "phastCons100way.UCSC.hg19")))
(build-system r-build-system)
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-genomicscores" ,r-genomicscores)
("r-iranges" ,r-iranges)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
(synopsis "UCSC phastCons conservation scores for hg19")
(description
"This package provides UCSC phastCons conservation scores for the human
genome (hg19) calculated from multiple alignments with other 99 vertebrate
species.")
(license license:artistic2.0)))
;;; Experiment data
(define-public r-abadata
(package
(name "r-abadata")
(version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ABAData" version 'experiment))
(sha256
(base32
"1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
(properties
`((upstream-name . "ABAData")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)))
(home-page "https://www.bioconductor.org/packages/ABAData/")
(synopsis "Gene expression in human brain regions from Allen Brain Atlas")
(description
"This package provides the data for the gene expression enrichment
analysis conducted in the package ABAEnrichment. The package includes three
datasets which are derived from the Allen Brain Atlas:
@enumerate
@item Gene expression data from Human Brain (adults) averaged across donors,
@item Gene expression data from the Developing Human Brain pooled into five
age categories and averaged across donors, and
@item a developmental effect score based on the Developing Human Brain
expression data.
@end enumerate
All datasets are restricted to protein coding genes.")
(license license:gpl2+)))
(define-public r-arrmdata
(package
(name "r-arrmdata")
(version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ARRmData" version 'experiment))
(sha256
(base32
"0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
(properties
`((upstream-name . "ARRmData")))
(build-system r-build-system)
(home-page "https://www.bioconductor.org/packages/ARRmData/")
(synopsis "Example dataset for normalization of Illumina 450k methylation data")
(description
"This package provides raw beta values from 36 samples across 3 groups
from Illumina 450k methylation arrays.")
(license license:artistic2.0)))
(define-public r-hsmmsinglecell
(package
(name "r-hsmmsinglecell")
(version "1.2.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
(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)))
(define-public r-all
(package
(name "r-all")
(version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ALL" version 'experiment))
(sha256
(base32
"1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
(properties `((upstream-name . "ALL")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)))
(home-page "https://bioconductor.org/packages/ALL")
(synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
(description
"The data consist of microarrays from 128 different individuals with
@dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
are available. The data have been normalized (using rma) and it is the
jointly normalized data that are available here. The data are presented in
the form of an @code{exprSet} object.")
(license license:artistic2.0)))
(define-public r-affydata
(package
(name "r-affydata")
(version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affydata" version 'experiment))
(sha256
(base32
"1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
(properties `((upstream-name . "affydata")))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)))
(home-page "https://bioconductor.org/packages/affydata/")
(synopsis "Affymetrix data for demonstration purposes")
(description
"This package provides example datasets that represent 'real world
examples' of Affymetrix data, unlike the artificial examples included in the
package @code{affy}.")
(license license:gpl2+)))
(define-public r-coverageview
(package
(name "r-coverageview")
(version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CoverageView" version))
(sha256
(base32
"0s47svs7xnr9jkylq0dxidqrigihdddiprcl0951vjr4w7kmb5nf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomicranges" ,r-genomicranges)
("r-genomicalignments" ,r-genomicalignments)
("r-rtracklayer" ,r-rtracklayer)
("r-rsamtools" ,r-rsamtools)))
(home-page "https://bioconductor.org/packages/CoverageView/")
(synopsis "Coverage visualization package for R")
(description "This package provides a framework for the visualization of
genome coverage profiles. It can be used for ChIP-seq experiments, but it can
be also used for genome-wide nucleosome positioning experiments or other
experiment types where it is important to have a framework in order to inspect
how the coverage distributed across the genome.")
(license license:artistic2.0)))
(define-public r-cummerbund
(package
(name "r-cummerbund")
(version "2.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "cummeRbund" version))
(sha256
(base32
"1fjc3bcclm4gsvw4nq6cv3a1kbrldvrxbkyfb9306708si1n4dwk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-fastcluster", r-fastcluster)
("r-ggplot2" ,r-ggplot2)
("r-gviz" ,r-gviz)
("r-plyr" ,r-plyr)
("r-reshape2" ,r-reshape2)
("r-rsqlite" ,r-rsqlite)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://bioconductor.org/packages/cummeRbund/")
(synopsis "Analyze Cufflinks high-throughput sequencing data")
(description "This package allows for persistent storage, access,
exploration, and manipulation of Cufflinks high-throughput sequencing
data. In addition, provides numerous plotting functions for commonly
used visualizations.")
(license license:artistic2.0)))
(define-public r-curatedtcgadata
(package
(name "r-curatedtcgadata")
(version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "curatedTCGAData" version 'experiment))
(sha256
(base32
"02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
(properties
`((upstream-name . "curatedTCGAData")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationhub" ,r-annotationhub)
("r-experimenthub" ,r-experimenthub)
("r-hdf5array" ,r-hdf5array)
("r-multiassayexperiment" ,r-multiassayexperiment)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)))
(home-page "https://bioconductor.org/packages/curatedTCGAData/")
(synopsis "Curated data from The Cancer Genome Atlas")
(description
"This package provides publicly available data from The Cancer Genome
Atlas (TCGA) as @code{MultiAssayExperiment} objects.
@code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
number, mutation, microRNA, protein, and others) with clinical / pathological
data. It also links assay barcodes with patient identifiers, enabling
harmonized subsetting of rows (features) and columns (patients / samples)
across the entire multi-'omics experiment.")
(license license:artistic2.0)))
;;; Packages
(define-public r-biocversion
(package
(name "r-biocversion")
(version "3.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocVersion" version))
(sha256
(base32
"0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f"))))
(properties `((upstream-name . "BiocVersion")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/BiocVersion/")
(synopsis "Set the appropriate version of Bioconductor packages")
(description
"This package provides repository information for the appropriate version
of Bioconductor.")
(license license:artistic2.0)))
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
(version "0.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocGenerics" version))
(sha256
(base32
"1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn"))))
(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-affycomp
(package
(name "r-affycomp")
(version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affycomp" version))
(sha256
(base32
"0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js"))))
(properties `((upstream-name . "affycomp")))
(build-system r-build-system)
(propagated-inputs `(("r-biobase" ,r-biobase)))
(home-page "https://bioconductor.org/packages/affycomp/")
(synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
(description
"The package contains functions that can be used to compare expression
measures for Affymetrix Oligonucleotide Arrays.")
(license license:gpl2+)))
(define-public r-affycompatible
(package
(name "r-affycompatible")
(version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AffyCompatible" version))
(sha256
(base32
"10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks"))))
(properties
`((upstream-name . "AffyCompatible")))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
("r-rcurl" ,r-rcurl)
("r-xml" ,r-xml)))
(home-page "https://bioconductor.org/packages/AffyCompatible/")
(synopsis "Work with Affymetrix GeneChip files")
(description
"This package provides an interface to Affymetrix chip annotation and
sample attribute files. The package allows an easy way for users to download
and manage local data bases of Affynmetrix NetAffx annotation files. It also
provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
Command Console} (AGCC)-compatible sample annotation files.")
(license license:artistic2.0)))
(define-public r-affycontam
(package
(name "r-affycontam")
(version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affyContam" version))
(sha256
(base32
"0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l"))))
(properties `((upstream-name . "affyContam")))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
("r-affydata" ,r-affydata)
("r-biobase" ,r-biobase)))
(home-page "https://bioconductor.org/packages/affyContam/")
(synopsis "Structured corruption of Affymetrix CEL file data")
(description
"Microarray quality assessment is a major concern of microarray analysts.
This package provides some simple approaches to in silico creation of quality
problems in CEL-level data to help evaluate performance of quality metrics.")
(license license:artistic2.0)))
(define-public r-affycoretools
(package
(name "r-affycoretools")
(version "1.58.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affycoretools" version))
(sha256
(base32
"1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw"))))
(properties `((upstream-name . "affycoretools")))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-dbi" ,r-dbi)
("r-edger" ,r-edger)
("r-gcrma" ,r-gcrma)
("r-glimma" ,r-glimma)
("r-ggplot2" ,r-ggplot2)
("r-gostats" ,r-gostats)
("r-gplots" ,r-gplots)
("r-hwriter" ,r-hwriter)
("r-lattice" ,r-lattice)
("r-limma" ,r-limma)
("r-oligoclasses" ,r-oligoclasses)
("r-reportingtools" ,r-reportingtools)
("r-rsqlite" ,r-rsqlite)
("r-s4vectors" ,r-s4vectors)
("r-xtable" ,r-xtable)))
(home-page "https://bioconductor.org/packages/affycoretools/")
(synopsis "Functions for analyses with Affymetrix GeneChips")
(description
"This package provides various wrapper functions that have been written
to streamline the more common analyses that a Biostatistician might see.")
(license license:artistic2.0)))
(define-public r-affxparser
(package
(name "r-affxparser")
(version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affxparser" version))
(sha256
(base32
"03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40"))))
(properties `((upstream-name . "affxparser")))
(build-system r-build-system)
(home-page "https://github.com/HenrikBengtsson/affxparser")
(synopsis "Affymetrix File Parsing SDK")
(description
"This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
BAR). It provides methods for fast and memory efficient parsing of Affymetrix
files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
are supported. Currently, there are methods for reading @dfn{chip definition
file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
either in full or in part. For example, probe signals from a few probesets
can be extracted very quickly from a set of CEL files into a convenient list
structure.")
;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
;; under LGPLv2+.
(license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
(define-public r-annotate
(package
(name "r-annotate")
(version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
"0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy"))))
(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 "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hpar" version))
(sha256
(base32
"1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m"))))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/hpar/")
(synopsis "Human Protein Atlas in R")
(description "This package provides a simple interface to and data from
the Human Protein Atlas project.")
(license license:artistic2.0)))
(define-public r-regioner
(package
(name "r-regioner")
(version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
"0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
("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")
(description "This package offers a statistical framework based on
customizable permutation tests to assess the association between genomic
region sets and other genomic features.")
(license license:artistic2.0)))
(define-public r-reportingtools
(package
(name "r-reportingtools")
(version "2.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReportingTools" version))
(sha256
(base32
"0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w"))))
(properties
`((upstream-name . "ReportingTools")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-category" ,r-category)
("r-deseq2" ,r-deseq2)
("r-edger" ,r-edger)
("r-ggbio" ,r-ggbio)
("r-ggplot2" ,r-ggplot2)
("r-gostats" ,r-gostats)
("r-gseabase" ,r-gseabase)
("r-hwriter" ,r-hwriter)
("r-iranges" ,r-iranges)
("r-knitr" ,r-knitr)
("r-lattice" ,r-lattice)
("r-limma" ,r-limma)
("r-pfam-db" ,r-pfam-db)
("r-r-utils" ,r-r-utils)
("r-xml" ,r-xml)))
(home-page "https://bioconductor.org/packages/ReportingTools/")
(synopsis "Tools for making reports in various formats")
(description
"The ReportingTools package enables users to easily display reports of
analysis results generated from sources such as microarray and sequencing
data. The package allows users to create HTML pages that may be viewed on a
web browser, or in other formats. Users can generate tables with sortable and
filterable columns, make and display plots, and link table entries to other
data sources such as NCBI or larger plots within the HTML page. Using the
package, users can also produce a table of contents page to link various
reports together for a particular project that can be viewed in a web
browser.")
(license license:artistic2.0)))
(define-public r-geneplotter
(package
(name "r-geneplotter")
(version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geneplotter" version))
(sha256
(base32
"1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx"))))
(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-oligoclasses
(package
(name "r-oligoclasses")
(version "1.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "oligoClasses" version))
(sha256
(base32
"02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf"))))
(properties `((upstream-name . "oligoClasses")))
(build-system r-build-system)
(propagated-inputs
`(("r-affyio" ,r-affyio)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-biocmanager" ,r-biocmanager)
("r-biostrings" ,r-biostrings)
("r-dbi" ,r-dbi)
("r-ff" ,r-ff)
("r-foreach" ,r-foreach)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-rsqlite" ,r-rsqlite)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)))
(home-page "https://bioconductor.org/packages/oligoClasses/")
(synopsis "Classes for high-throughput arrays")
(description
"This package contains class definitions, validity checks, and
initialization methods for classes used by the @code{oligo} and @code{crlmm}
packages.")
(license license:gpl2+)))
(define-public r-oligo
(package
(name "r-oligo")
(version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "oligo" version))
(sha256
(base32
"01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3"))))
(properties `((upstream-name . "oligo")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
(propagated-inputs
`(("r-affxparser" ,r-affxparser)
("r-affyio" ,r-affyio)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
("r-dbi" ,r-dbi)
("r-ff" ,r-ff)
("r-oligoclasses" ,r-oligoclasses)
("r-preprocesscore" ,r-preprocesscore)
("r-rsqlite" ,r-rsqlite)
("r-zlibbioc" ,r-zlibbioc)))
(home-page "https://bioconductor.org/packages/oligo/")
(synopsis "Preprocessing tools for oligonucleotide arrays")
(description
"This package provides a package to analyze oligonucleotide
arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
(license license:lgpl2.0+)))
(define-public r-qvalue
(package
(name "r-qvalue")
(version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "qvalue" version))
(sha256
(base32
"0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j"))))
(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 "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
"1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-amap" ,r-amap)
("r-biocparallel" ,r-biocparallel)
("r-deseq2" ,r-deseq2)
("r-dplyr" ,r-dplyr)
("r-edger" ,r-edger)
("r-genomicalignments" ,r-genomicalignments)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-ggrepel" ,r-ggrepel)
("r-gplots" ,r-gplots)
("r-iranges" ,r-iranges)
("r-lattice" ,r-lattice)
("r-limma" ,r-limma)
("r-locfit" ,r-locfit)
("r-rcolorbrewer" , r-rcolorbrewer)
("r-rcpp" ,r-rcpp)
("r-rhtslib" ,r-rhtslib)
("r-rsamtools" ,r-rsamtools)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-systempiper" ,r-systempiper)))
(home-page "https://bioconductor.org/packages/DiffBind")
(synopsis "Differential binding analysis of ChIP-Seq peak data")
(description
"This package computes differentially bound sites from multiple
ChIP-seq experiments using affinity (quantitative) data. Also enables
occupancy (overlap) analysis and plotting functions.")
(license license:artistic2.0)))
(define-public r-ripseeker
(package
(name "r-ripseeker")
(version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RIPSeeker" version))
(sha256
(base32
"1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
(properties `((upstream-name . "RIPSeeker")))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomicranges" ,r-genomicranges)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-rsamtools" ,r-rsamtools)
("r-genomicalignments" ,r-genomicalignments)
("r-rtracklayer" ,r-rtracklayer)))
(home-page "https://bioconductor.org/packages/RIPSeeker")
(synopsis
"Identifying protein-associated transcripts from RIP-seq experiments")
(description
"This package infers and discriminates RIP peaks from RIP-seq alignments
using two-state HMM with negative binomial emission probability. While
RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
a suite of bioinformatics tools integrated within this self-contained software
package comprehensively addressing issues ranging from post-alignments
processing to visualization and annotation.")
(license license:gpl2)))
(define-public r-multtest
(package
(name "r-multtest")
(version "2.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "multtest" version))
(sha256
(base32
"0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari"))))
(build-system r-build-system)
(propagated-inputs
`(("r-survival" ,r-survival)
("r-biocgenerics" ,r-biocgenerics)
("r-biobase" ,r-biobase)
("r-mass" ,r-mass)))
(home-page "https://bioconductor.org/packages/multtest")
(synopsis "Resampling-based multiple hypothesis testing")
(description
"This package can do non-parametric bootstrap and permutation
resampling-based multiple testing procedures (including empirical Bayes
methods) for controlling the family-wise error rate (FWER), generalized
family-wise error rate (gFWER), tail probability of the proportion of
false positives (TPPFP), and false discovery rate (FDR). Several choices
of bootstrap-based null distribution are implemented (centered, centered
and scaled, quantile-transformed). Single-step and step-wise methods are
available. Tests based on a variety of T- and F-statistics (including
T-statistics based on regression parameters from linear and survival models
as well as those based on correlation parameters) are included. When probing
hypotheses with T-statistics, users may also select a potentially faster null
distribution which is multivariate normal with mean zero and variance
covariance matrix derived from the vector influence function. Results are
reported in terms of adjusted P-values, confidence regions and test statistic
cutoffs. The procedures are directly applicable to identifying differentially
expressed genes in DNA microarray experiments.")
(license license:lgpl3)))
(define-public r-graph
(package
(name "r-graph")
(version "1.64.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "graph" version))
(sha256
(base32
"1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc"))))
(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)))
;; This is a CRAN package, but it depends on a Bioconductor package.
(define-public r-ggm
(package
(name "r-ggm")
(version "2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggm" version))
(sha256
(base32
"11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
(properties `((upstream-name . "ggm")))
(build-system r-build-system)
(propagated-inputs
`(("r-graph" ,r-graph)
("r-igraph" ,r-igraph)))
(home-page "https://cran.r-project.org/package=ggm")
(synopsis "Functions for graphical Markov models")
(description
"This package provides functions and datasets for maximum likelihood
fitting of some classes of graphical Markov models.")
(license license:gpl2+)))
(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 "https://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 "3.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
"0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-biocmanager" ,r-biocmanager)
("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-go-db" ,r-go-db)
("r-graph" ,r-graph)
("r-idr" ,r-idr)
("r-iranges" ,r-iranges)
("r-limma" ,r-limma)
("r-matrixstats" ,r-matrixstats)
("r-multtest" ,r-multtest)
("r-rbgl" ,r-rbgl)
("r-regioner" ,r-regioner)
("r-rsamtools" ,r-rsamtools)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-seqinr" ,r-seqinr)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-venndiagram" ,r-venndiagram)))
(home-page "https://bioconductor.org/packages/ChIPpeakAnno")
(synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
(description
"The package includes functions to retrieve the sequences around the peak,
obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
custom features such as most conserved elements and other transcription factor
binding sites supplied by users. Starting 2.0.5, new functions have been added
for finding the peaks with bi-directional promoters with summary statistics
(peaksNearBDP), for summarizing the occurrence of motifs in peaks
(summarizePatternInPeaks) and for adding other IDs to annotated peaks or
enrichedGO (addGeneIDs).")
(license license:gpl2+)))
(define-public r-marray
(package
(name "r-marray")
(version "1.64.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
(base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl"))))
(build-system r-build-system)
(propagated-inputs
`(("r-limma" ,r-limma)))
(home-page "https://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 functions for data input, diagnostic plots,
normalization and quality checking.")
(license license:lgpl2.0+)))
(define-public r-cghbase
(package
(name "r-cghbase")
(version "1.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
(base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-marray" ,r-marray)))
(home-page "https://bioconductor.org/packages/CGHbase")
(synopsis "Base functions and classes for arrayCGH data analysis")
(description "This package contains functions and classes that are needed by
the @code{arrayCGH} packages.")
(license license:gpl2+)))
(define-public r-cghcall
(package
(name "r-cghcall")
(version "2.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
(base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-cghbase" ,r-cghbase)
("r-impute" ,r-impute)
("r-dnacopy" ,r-dnacopy)
("r-snowfall" ,r-snowfall)))
(home-page "https://bioconductor.org/packages/CGHcall")
(synopsis "Base functions and classes for arrayCGH data analysis")
(description "This package contains functions and classes that are needed by
@code{arrayCGH} packages.")
(license license:gpl2+)))
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
(version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
(base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-cghbase" ,r-cghbase)
("r-cghcall" ,r-cghcall)
("r-dnacopy" ,r-dnacopy)
("r-future" ,r-future)
("r-future-apply" ,r-future-apply)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-matrixstats" ,r-matrixstats)
("r-r-utils" ,r-r-utils)
("r-rsamtools" ,r-rsamtools)))
(home-page "https://bioconductor.org/packages/QDNAseq")
(synopsis "Quantitative DNA sequencing for chromosomal aberrations")
(description "The genome is divided into non-overlapping fixed-sized bins,
number of sequence reads in each counted, adjusted with a simultaneous
two-dimensional loess correction for sequence mappability and GC content, and
filtered to remove spurious regions in the genome. Downstream steps of
segmentation and calling are also implemented via packages DNAcopy and CGHcall,
respectively.")
(license license:gpl2+)))
(define-public r-bayseq
(package
(name "r-bayseq")
(version "2.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "baySeq" version))
(sha256
(base32
"040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk"))))
(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 "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPComp" version))
(sha256
(base32
"0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg"))))
(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 "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RiboProfiling" version))
(sha256
(base32
"0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx"))))
(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 "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "riboSeqR" version))
(sha256
(base32
"1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm"))))
(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 "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "InteractionSet" version))
(sha256
(base32
"0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh"))))
(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 package 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 "1.20.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
"01ps97cs29qvzy5piq2l2k0yyr56rmg5cycfiqhbbvqpjrfvy60g"))))
(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)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(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 "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ctc" version))
(sha256
(base32
"0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d"))))
(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 "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "goseq" version))
(sha256
(base32
"11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv"))))
(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 "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Glimma" version))
(sha256
(base32
"1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r"))))
(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 "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ROTS" version))
(sha256
(base32
"08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm"))))
(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 "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "plgem" version))
(sha256
(base32
"0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v"))))
(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 "1.16.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "INSPEcT" version))
(sha256
(base32
"0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp"))))
(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-gdata" ,r-gdata)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicalignments" ,r-genomicalignments)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-kernsmooth" ,r-kernsmooth)
("r-plgem" ,r-plgem)
("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 "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNABarcodes" version))
(sha256
(base32
"0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd"))))
(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 "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RUVSeq" version))
(sha256
(base32
"1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj"))))
(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 "1.4.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocNeighbors" version))
(sha256
(base32
"1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6"))))
(properties `((upstream-name . "BiocNeighbors")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocparallel" ,r-biocparallel)
("r-matrix" ,r-matrix)
("r-rcpp" ,r-rcpp)
("r-rcppannoy" ,r-rcppannoy)
("r-rcpphnsw" ,r-rcpphnsw)
("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-biocsingular
(package
(name "r-biocsingular")
(version "1.2.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSingular" version))
(sha256
(base32
"1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407"))))
(properties `((upstream-name . "BiocSingular")))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
("r-biocgenerics" ,r-biocgenerics)
("r-biocparallel" ,r-biocparallel)
("r-delayedarray" ,r-delayedarray)
("r-irlba" ,r-irlba)
("r-matrix" ,r-matrix)
("r-rcpp" ,r-rcpp)
("r-rsvd" ,r-rsvd)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://github.com/LTLA/BiocSingular")
(synopsis "Singular value decomposition for Bioconductor packages")
(description
"This package implements exact and approximate methods for singular value
decomposition and principal components analysis, in a framework that allows
them to be easily switched within Bioconductor packages or workflows. Where
possible, parallelization is achieved using the BiocParallel framework.")
(license license:gpl3)))
(define-public r-destiny
(package
(name "r-destiny")
(version "3.0.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "destiny" version))
(sha256
(base32
"1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-ggplot-multistats" ,r-ggplot-multistats)
("r-ggplot2" ,r-ggplot2)
("r-ggthemes" ,r-ggthemes)
("r-irlba" ,r-irlba)
("r-knn-covertree" ,r-knn-covertree)
("r-matrix" ,r-matrix)
("r-pcamethods" ,r-pcamethods)
("r-proxy" ,r-proxy)
("r-rcpp" ,r-rcpp)
("r-rcppeigen" ,r-rcppeigen)
("r-rcpphnsw" ,r-rcpphnsw)
("r-rspectra" ,r-rspectra)
("r-scales" ,r-scales)
("r-scatterplot3d" ,r-scatterplot3d)
("r-singlecellexperiment" ,r-singlecellexperiment)
("r-smoother" ,r-smoother)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-tidyr" ,r-tidyr)
("r-tidyselect" ,r-tidyselect)
("r-vim" ,r-vim)))
(native-inputs
`(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
(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 "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "savR" version))
(sha256
(base32
"1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf"))))
(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 "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPexoQual" version))
(sha256
(base32
"044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0"))))
(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 "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "copynumber" version))
(sha256
(base32
"0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj"))))
(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 "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNAcopy" version))
(sha256
(base32
"119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw"))))
(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 "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEDS" version))
(sha256
(base32
"0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
(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)))
(define-public r-ebseq
(package
(name "r-ebseq")
(version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBSeq" version))
(sha256
(base32
"0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6"))))
(properties `((upstream-name . "EBSeq")))
(build-system r-build-system)
(propagated-inputs
`(("r-blockmodeling" ,r-blockmodeling)
("r-gplots" ,r-gplots)
("r-testthat" ,r-testthat)))
(home-page "https://bioconductor.org/packages/EBSeq")
(synopsis "Differential expression analysis of RNA-seq data")
(description
"This package provides tools for differential expression analysis at both
gene and isoform level using RNA-seq data")
(license license:artistic2.0)))
(define-public r-karyoploter
(package
(name "r-karyoploter")
(version "1.12.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "karyoploteR" version))
(sha256
(base32
"03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-regioner" ,r-regioner)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-rsamtools" ,r-rsamtools)
("r-memoise" ,r-memoise)
("r-rtracklayer" ,r-rtracklayer)
("r-genomeinfodb" ,r-genomeinfodb)
("r-s4vectors" ,r-s4vectors)
("r-biovizbase" ,r-biovizbase)
("r-digest" ,r-digest)
("r-bezier" ,r-bezier)
("r-bamsignals" ,r-bamsignals)
("r-annotationdbi" ,r-annotationdbi)
("r-variantannotation" ,r-variantannotation)))
(home-page "https://bioconductor.org/packages/karyoploteR/")
(synopsis "Plot customizable linear genomes displaying arbitrary data")
(description "This package creates karyotype plots of arbitrary genomes and
offers a complete set of functions to plot arbitrary data on them. It mimicks
many R base graphics functions coupling them with a coordinate change function
automatically mapping the chromosome and data coordinates into the plot
coordinates.")
(license license:artistic2.0)))
(define-public r-lpsymphony
(package
(name "r-lpsymphony")
(version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "lpsymphony" version))
(sha256
(base32
"0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv"))))
(build-system r-build-system)
(inputs
`(("gfortran" ,gfortran)
("zlib" ,zlib)))
(native-inputs