889 lines
34 KiB
Scheme
889 lines
34 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
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;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages bioconductor)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix build-system r)
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#:use-module (gnu packages)
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#:use-module (gnu packages bioinformatics)
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#:use-module (gnu packages cran)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages graph)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages web))
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(define-public r-bsgenome-dmelanogaster-ucsc-dm6
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(package
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(name "r-bsgenome-dmelanogaster-ucsc-dm6")
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(version "1.4.1")
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(source (origin
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(method url-fetch)
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;; We cannot use bioconductor-uri here because this tarball is
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;; located under "data/annotation/" instead of "bioc/".
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(uri (string-append "https://www.bioconductor.org/packages/"
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"release/data/annotation/src/contrib/"
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"BSgenome.Dmelanogaster.UCSC.dm6_"
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version ".tar.gz"))
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(sha256
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(base32
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"1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
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(properties
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`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
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(build-system r-build-system)
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;; As this package provides little more than a very large data file it
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;; doesn't make sense to build substitutes.
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(arguments `(#:substitutable? #f))
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(propagated-inputs
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`(("r-bsgenome" ,r-bsgenome)))
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(home-page
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"https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
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(synopsis "Full genome sequences for Fly")
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(description
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"This package provides full genome sequences for Drosophila
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melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
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objects.")
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(license license:artistic2.0)))
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(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
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(package
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(name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
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(version "1.3.99")
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(source (origin
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(method url-fetch)
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;; We cannot use bioconductor-uri here because this tarball is
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;; located under "data/annotation/" instead of "bioc/".
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(uri (string-append "http://www.bioconductor.org/packages/"
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"release/data/annotation/src/contrib/"
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"BSgenome.Dmelanogaster.UCSC.dm3.masked_"
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version ".tar.gz"))
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(sha256
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(base32
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"1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
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(properties
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`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-bsgenome" ,r-bsgenome)
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("r-bsgenome-dmelanogaster-ucsc-dm3"
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,r-bsgenome-dmelanogaster-ucsc-dm3)))
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(home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
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(synopsis "Full masked genome sequences for Fly")
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(description
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"This package provides full masked genome sequences for Drosophila
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melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
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Biostrings objects. The sequences are the same as in
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BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
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masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
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intra-contig ambiguities (AMB mask), (3) the mask of repeats from
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RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
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Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
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(license license:artistic2.0)))
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(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
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(package
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(name "r-bsgenome-hsapiens-ucsc-hg19-masked")
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(version "1.3.99")
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(source (origin
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(method url-fetch)
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;; We cannot use bioconductor-uri here because this tarball is
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;; located under "data/annotation/" instead of "bioc/".
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(uri (string-append "http://www.bioconductor.org/packages/"
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"release/data/annotation/src/contrib/"
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"BSgenome.Hsapiens.UCSC.hg19.masked_"
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version ".tar.gz"))
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(sha256
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||
(base32
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||
"0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
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(properties
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`((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-bsgenome" ,r-bsgenome)
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("r-bsgenome-hsapiens-ucsc-hg19"
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,r-bsgenome-hsapiens-ucsc-hg19)))
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(home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
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(synopsis "Full masked genome sequences for Homo sapiens")
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(description
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"This package provides full genome sequences for Homo sapiens (Human) as
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provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
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sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
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them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
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mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
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repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
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Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
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default.")
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(license license:artistic2.0)))
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(define-public r-bsgenome-mmusculus-ucsc-mm9-masked
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(package
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(name "r-bsgenome-mmusculus-ucsc-mm9-masked")
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(version "1.3.99")
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(source (origin
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(method url-fetch)
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;; We cannot use bioconductor-uri here because this tarball is
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;; located under "data/annotation/" instead of "bioc/".
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(uri (string-append "http://www.bioconductor.org/packages/"
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"release/data/annotation/src/contrib/"
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"BSgenome.Mmusculus.UCSC.mm9.masked_"
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version ".tar.gz"))
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(sha256
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(base32
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"00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
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(properties
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`((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-bsgenome" ,r-bsgenome)
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("r-bsgenome-mmusculus-ucsc-mm9"
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,r-bsgenome-mmusculus-ucsc-mm9)))
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(home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
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(synopsis "Full masked genome sequences for Mouse")
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(description
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"This package provides full genome sequences for Mus musculus (Mouse) as
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provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
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sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
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them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
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mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
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repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
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Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
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default." )
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(license license:artistic2.0)))
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(define-public r-genelendatabase
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(package
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(name "r-genelendatabase")
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(version "1.16.0")
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(source
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(origin
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(method url-fetch)
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;; We cannot use bioconductor-uri here because this tarball is
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;; located under "data/experiment/" instead of "bioc/".
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(uri (string-append "https://bioconductor.org/packages/"
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"release/data/experiment/src/contrib"
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"/geneLenDataBase_" version ".tar.gz"))
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(sha256
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(base32
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"07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5"))))
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(properties
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`((upstream-name . "geneLenDataBase")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-rtracklayer" ,r-rtracklayer)
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("r-genomicfeatures" ,r-genomicfeatures)))
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(home-page "https://bioconductor.org/packages/geneLenDataBase/")
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(synopsis "Lengths of mRNA transcripts for a number of genomes")
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(description
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"This package provides the lengths of mRNA transcripts for a number of
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genomes and gene ID formats, largely based on the UCSC table browser.")
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(license license:lgpl2.0+)))
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(define-public r-hpar
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(package
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(name "r-hpar")
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(version "1.22.2")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "hpar" version))
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||
(sha256
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||
(base32
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"1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
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(build-system r-build-system)
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(home-page "https://bioconductor.org/packages/hpar/")
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||
(synopsis "Human Protein Atlas in R")
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||
(description "This package provides a simple interface to and data from
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the Human Protein Atlas project.")
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(license license:artistic2.0)))
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(define-public r-regioner
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(package
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(name "r-regioner")
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(version "1.12.0")
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||
(source
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(origin
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||
(method url-fetch)
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||
(uri (bioconductor-uri "regioneR" version))
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||
(sha256
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||
(base32
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||
"09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
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||
(properties `((upstream-name . "regioneR")))
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||
(build-system r-build-system)
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||
(propagated-inputs
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||
`(("r-memoise" ,r-memoise)
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||
("r-genomicranges" ,r-genomicranges)
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||
("r-bsgenome" ,r-bsgenome)
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||
("r-rtracklayer" ,r-rtracklayer)
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("r-genomeinfodb" ,r-genomeinfodb)
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||
("r-iranges" ,r-iranges)
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("r-s4vectors" ,r-s4vectors)))
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||
(home-page "https://bioconductor.org/packages/regioneR/")
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||
(synopsis "Association analysis of genomic regions")
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||
(description "This package offers a statistical framework based on
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customizable permutation tests to assess the association between genomic
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region sets and other genomic features.")
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(license license:artistic2.0)))
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(define-public r-diffbind
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(package
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(name "r-diffbind")
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(version "2.8.0")
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(source
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||
(origin
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||
(method url-fetch)
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||
(uri (bioconductor-uri "DiffBind" version))
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||
(sha256
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||
(base32
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||
"1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
|
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(properties `((upstream-name . "DiffBind")))
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||
(build-system r-build-system)
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(inputs
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||
`(("zlib" ,zlib)))
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(propagated-inputs
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`(("r-amap" ,r-amap)
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("r-biocparallel" ,r-biocparallel)
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("r-deseq2" ,r-deseq2)
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("r-dplyr" ,r-dplyr)
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("r-edger" ,r-edger)
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("r-genomicalignments" ,r-genomicalignments)
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("r-genomicranges" ,r-genomicranges)
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("r-ggplot2" ,r-ggplot2)
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("r-ggrepel" ,r-ggrepel)
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("r-gplots" ,r-gplots)
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("r-iranges" ,r-iranges)
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("r-lattice" ,r-lattice)
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("r-limma" ,r-limma)
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("r-locfit" ,r-locfit)
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("r-rcolorbrewer" , r-rcolorbrewer)
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("r-rcpp" ,r-rcpp)
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("r-rsamtools" ,r-rsamtools)
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("r-s4vectors" ,r-s4vectors)
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||
("r-summarizedexperiment" ,r-summarizedexperiment)
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("r-systempiper" ,r-systempiper)
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("r-zlibbioc" ,r-zlibbioc)))
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||
(home-page "http://bioconductor.org/packages/DiffBind")
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||
(synopsis "Differential binding analysis of ChIP-Seq peak data")
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||
(description
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"This package computes differentially bound sites from multiple
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ChIP-seq experiments using affinity (quantitative) data. Also enables
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occupancy (overlap) analysis and plotting functions.")
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(license license:artistic2.0)))
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||
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(define-public r-ripseeker
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(package
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(name "r-ripseeker")
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(version "1.20.0")
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(source
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||
(origin
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||
(method url-fetch)
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||
(uri (bioconductor-uri "RIPSeeker" version))
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||
(sha256
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||
(base32
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||
"0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
|
||
(properties `((upstream-name . "RIPSeeker")))
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||
(build-system r-build-system)
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||
(propagated-inputs
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||
`(("r-s4vectors" ,r-s4vectors)
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||
("r-iranges" ,r-iranges)
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||
("r-genomicranges" ,r-genomicranges)
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||
("r-summarizedexperiment" ,r-summarizedexperiment)
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||
("r-rsamtools" ,r-rsamtools)
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||
("r-genomicalignments" ,r-genomicalignments)
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("r-rtracklayer" ,r-rtracklayer)))
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||
(home-page "http://bioconductor.org/packages/RIPSeeker")
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||
(synopsis
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"Identifying protein-associated transcripts from RIP-seq experiments")
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||
(description
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||
"This package infers and discriminates RIP peaks from RIP-seq alignments
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using two-state HMM with negative binomial emission probability. While
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RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
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a suite of bioinformatics tools integrated within this self-contained software
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package comprehensively addressing issues ranging from post-alignments
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processing to visualization and annotation.")
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||
(license license:gpl2)))
|
||
|
||
(define-public r-multtest
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||
(package
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||
(name "r-multtest")
|
||
(version "2.36.0")
|
||
(source
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||
(origin
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||
(method url-fetch)
|
||
(uri (bioconductor-uri "multtest" version))
|
||
(sha256
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||
(base32
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||
"11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
|
||
(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 "http://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 "1.58.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "graph" version))
|
||
(sha256
|
||
(base32
|
||
"1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
|
||
(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
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||
(name "r-codedepends")
|
||
(version "0.6.5")
|
||
(source
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||
(origin
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||
(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
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||
(name "r-chippeakanno")
|
||
(version "3.14.2")
|
||
(source
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||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPpeakAnno" version))
|
||
(sha256
|
||
(base32
|
||
"13rksc65lxxzyw11galh6xzvgzp5ii0gwiwpvrm395v2r17rhwsc"))))
|
||
(properties `((upstream-name . "ChIPpeakAnno")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-delayedarray" ,r-delayedarray)
|
||
("r-go-db" ,r-go-db)
|
||
("r-biomart" ,r-biomart)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-iranges" ,r-iranges)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-annotationdbi" ,r-annotationdbi)
|
||
("r-limma" ,r-limma)
|
||
("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)
|
||
("r-biobase" ,r-biobase)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-seqinr" ,r-seqinr)
|
||
("r-idr" ,r-idr)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-venndiagram" ,r-venndiagram)))
|
||
(home-page "http://bioconductor.org/packages/ChIPpeakAnno")
|
||
(synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
|
||
(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 "1.58.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "marray" version))
|
||
(sha256
|
||
(base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-limma" ,r-limma)))
|
||
(home-page "http://bioconductor.org/packages/marray")
|
||
(synopsis "Exploratory analysis for two-color spotted microarray data")
|
||
(description "This package contains class definitions for two-color spotted
|
||
microarray data. It also includes fuctions for data input, diagnostic plots,
|
||
normalization and quality checking.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-cghbase
|
||
(package
|
||
(name "r-cghbase")
|
||
(version "1.40.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "CGHbase" version))
|
||
(sha256
|
||
(base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
|
||
(properties `((upstream-name . "CGHbase")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-marray" ,r-marray)))
|
||
(home-page "http://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 "2.42.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "CGHcall" version))
|
||
(sha256
|
||
(base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
|
||
(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 "http://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 "1.16.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "QDNAseq" version))
|
||
(sha256
|
||
(base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
|
||
(properties `((upstream-name . "QDNAseq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-cghbase" ,r-cghbase)
|
||
("r-cghcall" ,r-cghcall)
|
||
("r-dnacopy" ,r-dnacopy)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-r-utils" ,r-r-utils)
|
||
("r-rsamtools" ,r-rsamtools)))
|
||
(home-page "http://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 "2.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "baySeq" version))
|
||
(sha256
|
||
(base32
|
||
"0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
|
||
(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 "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPComp" version))
|
||
(sha256
|
||
(base32
|
||
"0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
|
||
(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 "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RiboProfiling" version))
|
||
(sha256
|
||
(base32
|
||
"04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
|
||
(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 "1.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "riboSeqR" version))
|
||
(sha256
|
||
(base32
|
||
"0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
|
||
(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 "1.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "InteractionSet" version))
|
||
(sha256
|
||
(base32
|
||
"0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
|
||
(properties
|
||
`((upstream-name . "InteractionSet")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-matrix" ,r-matrix)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://bioconductor.org/packages/InteractionSet")
|
||
(synopsis "Base classes for storing genomic interaction data")
|
||
(description
|
||
"This packages provides the @code{GInteractions},
|
||
@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
|
||
for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
|
||
experiments.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-genomicinteractions
|
||
(package
|
||
(name "r-genomicinteractions")
|
||
(version "1.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GenomicInteractions" version))
|
||
(sha256
|
||
(base32
|
||
"0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
|
||
(properties
|
||
`((upstream-name . "GenomicInteractions")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-data-table" ,r-data-table)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-gviz" ,r-gviz)
|
||
("r-igraph" ,r-igraph)
|
||
("r-interactionset" ,r-interactionset)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-stringr" ,r-stringr)))
|
||
(home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
|
||
(synopsis "R package for handling genomic interaction data")
|
||
(description
|
||
"This R package provides tools for handling genomic interaction data,
|
||
such as ChIA-PET/Hi-C, annotating genomic features with interaction
|
||
information and producing various plots and statistics.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-ctc
|
||
(package
|
||
(name "r-ctc")
|
||
(version "1.54.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ctc" version))
|
||
(sha256
|
||
(base32
|
||
"0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9"))))
|
||
(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 "1.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "goseq" version))
|
||
(sha256
|
||
(base32
|
||
"0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l"))))
|
||
(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 "1.8.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Glimma" version))
|
||
(sha256
|
||
(base32
|
||
"0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s"))))
|
||
(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 "1.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ROTS" version))
|
||
(sha256
|
||
(base32
|
||
"12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3"))))
|
||
(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-inspect
|
||
(package
|
||
(name "r-inspect")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "INSPEcT" version))
|
||
(sha256
|
||
(base32
|
||
"1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p"))))
|
||
(properties `((upstream-name . "INSPEcT")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-desolve" ,r-desolve)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-preprocesscore" ,r-preprocesscore)
|
||
("r-proc" ,r-proc)
|
||
("r-rootsolve" ,r-rootsolve)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(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)))
|