2885 lines
109 KiB
Scheme
2885 lines
109 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
|
||
;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
|
||
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
|
||
;;;
|
||
;;; This file is part of GNU Guix.
|
||
;;;
|
||
;;; 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 build-system r)
|
||
#:use-module (gnu packages)
|
||
#:use-module (gnu packages bioinformatics)
|
||
#:use-module (gnu packages cran)
|
||
#:use-module (gnu packages compression)
|
||
#:use-module (gnu packages gcc)
|
||
#:use-module (gnu packages graph)
|
||
#:use-module (gnu packages maths)
|
||
#:use-module (gnu packages pkg-config)
|
||
#:use-module (gnu packages statistics)
|
||
#:use-module (gnu packages web))
|
||
|
||
|
||
;;; Annotations
|
||
|
||
(define-public r-bsgenome-celegans-ucsc-ce6
|
||
(package
|
||
(name "r-bsgenome-celegans-ucsc-ce6")
|
||
(version "1.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Celegans.UCSC.ce6_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
|
||
(build-system r-build-system)
|
||
;; As this package provides little more than a very large data file it
|
||
;; doesn't make sense to build substitutes.
|
||
(arguments `(#:substitutable? #f))
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)))
|
||
(home-page
|
||
"https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
|
||
(synopsis "Full genome sequences for Worm")
|
||
(description
|
||
"This package provides full genome sequences for Caenorhabditis
|
||
elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
|
||
objects.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-bsgenome-celegans-ucsc-ce10
|
||
(package
|
||
(name "r-bsgenome-celegans-ucsc-ce10")
|
||
(version "1.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Celegans.UCSC.ce10_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
|
||
(build-system r-build-system)
|
||
;; As this package provides little more than a very large data file it
|
||
;; doesn't make sense to build substitutes.
|
||
(arguments `(#:substitutable? #f))
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)))
|
||
(home-page
|
||
"https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
|
||
(synopsis "Full genome sequences for Worm")
|
||
(description
|
||
"This package provides full genome sequences for Caenorhabditis
|
||
elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
|
||
objects.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-bsgenome-dmelanogaster-ucsc-dm6
|
||
(package
|
||
(name "r-bsgenome-dmelanogaster-ucsc-dm6")
|
||
(version "1.4.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Dmelanogaster.UCSC.dm6_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
|
||
(build-system r-build-system)
|
||
;; As this package provides little more than a very large data file it
|
||
;; doesn't make sense to build substitutes.
|
||
(arguments `(#:substitutable? #f))
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)))
|
||
(home-page
|
||
"https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.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)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Dmelanogaster.UCSC.dm3_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
|
||
(build-system r-build-system)
|
||
;; As this package provides little more than a very large data file it
|
||
;; doesn't make sense to build substitutes.
|
||
(arguments `(#:substitutable? #f))
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)))
|
||
(home-page
|
||
"https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
|
||
(synopsis "Full genome sequences for Fly")
|
||
(description
|
||
"This package provides full genome sequences for Drosophila
|
||
melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
|
||
Biostrings objects.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
|
||
(package
|
||
(name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
|
||
(version "1.3.99")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "http://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Dmelanogaster.UCSC.dm3.masked_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)
|
||
("r-bsgenome-dmelanogaster-ucsc-dm3"
|
||
,r-bsgenome-dmelanogaster-ucsc-dm3)))
|
||
(home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
|
||
(synopsis "Full masked genome sequences for Fly")
|
||
(description
|
||
"This package provides full masked genome sequences for Drosophila
|
||
melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
|
||
Biostrings objects. The sequences are the same as in
|
||
BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
|
||
masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
|
||
intra-contig ambiguities (AMB mask), (3) the mask of repeats from
|
||
RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
|
||
Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-bsgenome-hsapiens-1000genomes-hs37d5
|
||
(package
|
||
(name "r-bsgenome-hsapiens-1000genomes-hs37d5")
|
||
(version "0.99.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Hsapiens.1000genomes.hs37d5_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
|
||
(build-system r-build-system)
|
||
;; As this package provides little more than a very large data file it
|
||
;; doesn't make sense to build substitutes.
|
||
(arguments `(#:substitutable? #f))
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)))
|
||
(home-page
|
||
"https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
|
||
(synopsis "Full genome sequences for Homo sapiens")
|
||
(description
|
||
"This package provides full genome sequences for Homo sapiens from
|
||
1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
|
||
(package
|
||
(name "r-bsgenome-hsapiens-ucsc-hg19-masked")
|
||
(version "1.3.99")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "http://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Hsapiens.UCSC.hg19.masked_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)
|
||
("r-bsgenome-hsapiens-ucsc-hg19"
|
||
,r-bsgenome-hsapiens-ucsc-hg19)))
|
||
(home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
|
||
(synopsis "Full masked genome sequences for Homo sapiens")
|
||
(description
|
||
"This package provides full genome sequences for Homo sapiens (Human) as
|
||
provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
|
||
sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
|
||
them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
|
||
mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
|
||
repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
|
||
Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
|
||
default.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-bsgenome-mmusculus-ucsc-mm9
|
||
(package
|
||
(name "r-bsgenome-mmusculus-ucsc-mm9")
|
||
(version "1.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Mmusculus.UCSC.mm9_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
|
||
(build-system r-build-system)
|
||
;; As this package provides little more than a very large data file it
|
||
;; doesn't make sense to build substitutes.
|
||
(arguments `(#:substitutable? #f))
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)))
|
||
(home-page
|
||
"https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
|
||
(synopsis "Full genome sequences for Mouse")
|
||
(description
|
||
"This package provides full genome sequences for Mus musculus (Mouse) as
|
||
provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-bsgenome-mmusculus-ucsc-mm9-masked
|
||
(package
|
||
(name "r-bsgenome-mmusculus-ucsc-mm9-masked")
|
||
(version "1.3.99")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "http://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Mmusculus.UCSC.mm9.masked_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)
|
||
("r-bsgenome-mmusculus-ucsc-mm9"
|
||
,r-bsgenome-mmusculus-ucsc-mm9)))
|
||
(home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
|
||
(synopsis "Full masked genome sequences for Mouse")
|
||
(description
|
||
"This package provides full genome sequences for Mus musculus (Mouse) as
|
||
provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
|
||
sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
|
||
them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
|
||
mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
|
||
repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
|
||
Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
|
||
default." )
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-bsgenome-mmusculus-ucsc-mm10
|
||
(package
|
||
(name "r-bsgenome-mmusculus-ucsc-mm10")
|
||
(version "1.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Mmusculus.UCSC.mm10_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
|
||
(build-system r-build-system)
|
||
;; As this package provides little more than a very large data file it
|
||
;; doesn't make sense to build substitutes.
|
||
(arguments `(#:substitutable? #f))
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)))
|
||
(home-page
|
||
"https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
|
||
(synopsis "Full genome sequences for Mouse")
|
||
(description
|
||
"This package provides full genome sequences for Mus
|
||
musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
|
||
in Biostrings objects.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-org-ce-eg-db
|
||
(package
|
||
(name "r-org-ce-eg-db")
|
||
(version "3.7.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"org.Ce.eg.db_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
|
||
(properties
|
||
`((upstream-name . "org.Ce.eg.db")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)))
|
||
(home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
|
||
(synopsis "Genome wide annotation for Worm")
|
||
(description
|
||
"This package provides mappings from Entrez gene identifiers to various
|
||
annotations for the genome of the model worm Caenorhabditis elegans.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-org-dm-eg-db
|
||
(package
|
||
(name "r-org-dm-eg-db")
|
||
(version "3.7.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"org.Dm.eg.db_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
|
||
(properties
|
||
`((upstream-name . "org.Dm.eg.db")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)))
|
||
(home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
|
||
(synopsis "Genome wide annotation for Fly")
|
||
(description
|
||
"This package provides mappings from Entrez gene identifiers to various
|
||
annotations for the genome of the model fruit fly Drosophila melanogaster.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-org-dr-eg-db
|
||
(package
|
||
(name "r-org-dr-eg-db")
|
||
(version "3.7.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"org.Dr.eg.db_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
|
||
(properties
|
||
`((upstream-name . "org.Dr.eg.db")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)))
|
||
(home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
|
||
(synopsis "Annotation for Zebrafish")
|
||
(description
|
||
"This package provides genome wide annotations for Zebrafish, primarily
|
||
based on mapping using Entrez Gene identifiers.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-org-hs-eg-db
|
||
(package
|
||
(name "r-org-hs-eg-db")
|
||
(version "3.7.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"org.Hs.eg.db_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
|
||
(properties
|
||
`((upstream-name . "org.Hs.eg.db")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)))
|
||
(home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
|
||
(synopsis "Genome wide annotation for Human")
|
||
(description
|
||
"This package contains genome-wide annotations for Human, primarily based
|
||
on mapping using Entrez Gene identifiers.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-org-mm-eg-db
|
||
(package
|
||
(name "r-org-mm-eg-db")
|
||
(version "3.7.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"org.Mm.eg.db_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
|
||
(properties
|
||
`((upstream-name . "org.Mm.eg.db")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)))
|
||
(home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
|
||
(synopsis "Genome wide annotation for Mouse")
|
||
(description
|
||
"This package provides mappings from Entrez gene identifiers to various
|
||
annotations for the genome of the model mouse Mus musculus.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-bsgenome-hsapiens-ucsc-hg19
|
||
(package
|
||
(name "r-bsgenome-hsapiens-ucsc-hg19")
|
||
(version "1.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"BSgenome.Hsapiens.UCSC.hg19_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
|
||
(build-system r-build-system)
|
||
;; As this package provides little more than a very large data file it
|
||
;; doesn't make sense to build substitutes.
|
||
(arguments `(#:substitutable? #f))
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)))
|
||
(home-page
|
||
"https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
|
||
(synopsis "Full genome sequences for Homo sapiens")
|
||
(description
|
||
"This package provides full genome sequences for Homo sapiens as provided
|
||
by UCSC (hg19, February 2009) and stored in Biostrings objects.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-genelendatabase
|
||
(package
|
||
(name "r-genelendatabase")
|
||
(version "1.18.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/experiment/" instead of "bioc/".
|
||
(uri (string-append "https://bioconductor.org/packages/"
|
||
"release/data/experiment/src/contrib"
|
||
"/geneLenDataBase_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
|
||
(properties
|
||
`((upstream-name . "geneLenDataBase")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-rtracklayer" ,r-rtracklayer)
|
||
("r-genomicfeatures" ,r-genomicfeatures)))
|
||
(home-page "https://bioconductor.org/packages/geneLenDataBase/")
|
||
(synopsis "Lengths of mRNA transcripts for a number of genomes")
|
||
(description
|
||
"This package provides the lengths of mRNA transcripts for a number of
|
||
genomes and gene ID formats, largely based on the UCSC table browser.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-txdb-hsapiens-ucsc-hg19-knowngene
|
||
(package
|
||
(name "r-txdb-hsapiens-ucsc-hg19-knowngene")
|
||
(version "3.2.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib"
|
||
"/TxDb.Hsapiens.UCSC.hg19.knownGene_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
|
||
(properties
|
||
`((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
|
||
(build-system r-build-system)
|
||
;; As this package provides little more than a very large data file it
|
||
;; doesn't make sense to build substitutes.
|
||
(arguments `(#:substitutable? #f))
|
||
(propagated-inputs
|
||
`(("r-genomicfeatures" ,r-genomicfeatures)))
|
||
(home-page
|
||
"https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
|
||
(synopsis "Annotation package for human genome in TxDb format")
|
||
(description
|
||
"This package provides an annotation database of Homo sapiens genome
|
||
data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
|
||
track. The database is exposed as a @code{TxDb} object.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-txdb-mmusculus-ucsc-mm9-knowngene
|
||
(package
|
||
(name "r-txdb-mmusculus-ucsc-mm9-knowngene")
|
||
(version "3.2.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib"
|
||
"/TxDb.Mmusculus.UCSC.mm9.knownGene_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
|
||
(properties
|
||
`((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-annotationdbi" ,r-annotationdbi)))
|
||
(home-page
|
||
"https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
|
||
(synopsis "Annotation package for mouse genome in TxDb format")
|
||
(description
|
||
"This package provides an annotation database of Mouse genome data. It
|
||
is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
|
||
database is exposed as a @code{TxDb} object.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
|
||
(package
|
||
(name "r-txdb-mmusculus-ucsc-mm10-knowngene")
|
||
(version "3.4.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"TxDb.Mmusculus.UCSC.mm10.knownGene_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
|
||
(properties
|
||
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
|
||
(build-system r-build-system)
|
||
;; As this package provides little more than a very large data file it
|
||
;; doesn't make sense to build substitutes.
|
||
(arguments `(#:substitutable? #f))
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-annotationdbi" ,r-annotationdbi)))
|
||
(home-page
|
||
"https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
|
||
(synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
|
||
(description
|
||
"This package loads a TxDb object, which is an R interface to
|
||
prefabricated databases contained in this package. This package provides
|
||
the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
|
||
based on the knownGene track.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-fdb-infiniummethylation-hg19
|
||
(package
|
||
(name "r-fdb-infiniummethylation-hg19")
|
||
(version "2.2.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"FDb.InfiniumMethylation.hg19_"
|
||
version ".tar.gz"))
|
||
(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)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"IlluminaHumanMethylationEPICmanifest_"
|
||
version ".tar.gz"))
|
||
(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-do-db
|
||
(package
|
||
(name "r-do-db")
|
||
(version "2.9")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/annotation/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/annotation/src/contrib/"
|
||
"DO.db_" version ".tar.gz"))
|
||
(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)))
|
||
|
||
|
||
;;; Experiment data
|
||
|
||
(define-public r-hsmmsinglecell
|
||
(package
|
||
(name "r-hsmmsinglecell")
|
||
(version "1.2.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; We cannot use bioconductor-uri here because this tarball is
|
||
;; located under "data/experiment/" instead of "bioc/".
|
||
(uri (string-append "https://www.bioconductor.org/packages/"
|
||
"release/data/experiment/src/contrib/"
|
||
"HSMMSingleCell_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
|
||
(properties
|
||
`((upstream-name . "HSMMSingleCell")))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
|
||
(synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
|
||
(description
|
||
"Skeletal myoblasts undergo a well-characterized sequence of
|
||
morphological and transcriptional changes during differentiation. In this
|
||
experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
|
||
under high mitogen conditions (GM) and then differentiated by switching to
|
||
low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
|
||
hundred cells taken over a time-course of serum-induced differentiation.
|
||
Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
|
||
72 hours) following serum switch using the Fluidigm C1 microfluidic system.
|
||
RNA from each cell was isolated and used to construct mRNA-Seq libraries,
|
||
which were then sequenced to a depth of ~4 million reads per library,
|
||
resulting in a complete gene expression profile for each cell.")
|
||
(license license:artistic2.0)))
|
||
|
||
|
||
;;; Packages
|
||
|
||
(define-public r-biocgenerics
|
||
(package
|
||
(name "r-biocgenerics")
|
||
(version "0.28.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "BiocGenerics" version))
|
||
(sha256
|
||
(base32
|
||
"0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
|
||
(properties
|
||
`((upstream-name . "BiocGenerics")))
|
||
(build-system r-build-system)
|
||
(home-page "https://bioconductor.org/packages/BiocGenerics")
|
||
(synopsis "S4 generic functions for Bioconductor")
|
||
(description
|
||
"This package provides S4 generic functions needed by many Bioconductor
|
||
packages.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-annotate
|
||
(package
|
||
(name "r-annotate")
|
||
(version "1.60.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "annotate" version))
|
||
(sha256
|
||
(base32
|
||
"0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"))))
|
||
(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 "1.24.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "hpar" version))
|
||
(sha256
|
||
(base32
|
||
"1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
|
||
(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 "1.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "regioneR" version))
|
||
(sha256
|
||
(base32
|
||
"19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
|
||
(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-geneplotter
|
||
(package
|
||
(name "r-geneplotter")
|
||
(version "1.60.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "geneplotter" version))
|
||
(sha256
|
||
(base32
|
||
"10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotate" ,r-annotate)
|
||
("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-lattice" ,r-lattice)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)))
|
||
(home-page "https://bioconductor.org/packages/geneplotter")
|
||
(synopsis "Graphics functions for genomic data")
|
||
(description
|
||
"This package provides functions for plotting genomic data.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-qvalue
|
||
(package
|
||
(name "r-qvalue")
|
||
(version "2.14.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "qvalue" version))
|
||
(sha256
|
||
(base32
|
||
"0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-ggplot2" ,r-ggplot2)
|
||
("r-reshape2" ,r-reshape2)))
|
||
(home-page "http://github.com/jdstorey/qvalue")
|
||
(synopsis "Q-value estimation for false discovery rate control")
|
||
(description
|
||
"This package takes a list of p-values resulting from the simultaneous
|
||
testing of many hypotheses and estimates their q-values and local @dfn{false
|
||
discovery rate} (FDR) values. The q-value of a test measures the proportion
|
||
of false positives incurred when that particular test is called significant.
|
||
The local FDR measures the posterior probability the null hypothesis is true
|
||
given the test's p-value. Various plots are automatically generated, allowing
|
||
one to make sensible significance cut-offs. The software can be applied to
|
||
problems in genomics, brain imaging, astrophysics, and data mining.")
|
||
;; Any version of the LGPL.
|
||
(license license:lgpl3+)))
|
||
|
||
(define-public r-diffbind
|
||
(package
|
||
(name "r-diffbind")
|
||
(version "2.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DiffBind" version))
|
||
(sha256
|
||
(base32
|
||
"0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
|
||
(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-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-systempiper" ,r-systempiper)
|
||
("r-zlibbioc" ,r-zlibbioc)))
|
||
(home-page "http://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 "1.22.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RIPSeeker" version))
|
||
(sha256
|
||
(base32
|
||
"1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
|
||
(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 "http://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 "2.38.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "multtest" version))
|
||
(sha256
|
||
(base32
|
||
"0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
|
||
(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 "1.60.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "graph" version))
|
||
(sha256
|
||
(base32
|
||
"1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)))
|
||
(home-page "https://bioconductor.org/packages/graph")
|
||
(synopsis "Handle graph data structures in R")
|
||
(description
|
||
"This package implements some simple graph handling capabilities for R.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-codedepends
|
||
(package
|
||
(name "r-codedepends")
|
||
(version "0.6.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "CodeDepends" version))
|
||
(sha256
|
||
(base32
|
||
"0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
|
||
(properties `((upstream-name . "CodeDepends")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-codetools" ,r-codetools)
|
||
("r-graph" ,r-graph)
|
||
("r-xml" ,r-xml)))
|
||
(home-page "http://cran.r-project.org/web/packages/CodeDepends")
|
||
(synopsis "Analysis of R code for reproducible research and code comprehension")
|
||
(description
|
||
"This package provides tools for analyzing R expressions or blocks of
|
||
code and determining the dependencies between them. It focuses on R scripts,
|
||
but can be used on the bodies of functions. There are many facilities
|
||
including the ability to summarize or get a high-level view of code,
|
||
determining dependencies between variables, code improvement suggestions.")
|
||
;; Any version of the GPL
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-chippeakanno
|
||
(package
|
||
(name "r-chippeakanno")
|
||
(version "3.16.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPpeakAnno" version))
|
||
(sha256
|
||
(base32
|
||
"1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
|
||
(properties `((upstream-name . "ChIPpeakAnno")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocmanager" ,r-biocmanager)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-delayedarray" ,r-delayedarray)
|
||
("r-go-db" ,r-go-db)
|
||
("r-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-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 "1.60.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "marray" version))
|
||
(sha256
|
||
(base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
|
||
(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 "1.42.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "CGHbase" version))
|
||
(sha256
|
||
(base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
|
||
(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 "2.44.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "CGHcall" version))
|
||
(sha256
|
||
(base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
|
||
(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 "1.18.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "QDNAseq" version))
|
||
(sha256
|
||
(base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
|
||
(properties `((upstream-name . "QDNAseq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-cghbase" ,r-cghbase)
|
||
("r-cghcall" ,r-cghcall)
|
||
("r-dnacopy" ,r-dnacopy)
|
||
("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 "2.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "baySeq" version))
|
||
(sha256
|
||
(base32
|
||
"0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
|
||
(properties `((upstream-name . "baySeq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-abind" ,r-abind)
|
||
("r-edger" ,r-edger)
|
||
("r-genomicranges" ,r-genomicranges)))
|
||
(home-page "https://bioconductor.org/packages/baySeq/")
|
||
(synopsis "Bayesian analysis of differential expression patterns in count data")
|
||
(description
|
||
"This package identifies differential expression in high-throughput count
|
||
data, such as that derived from next-generation sequencing machines,
|
||
calculating estimated posterior likelihoods of differential expression (or
|
||
more complex hypotheses) via empirical Bayesian methods.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-chipcomp
|
||
(package
|
||
(name "r-chipcomp")
|
||
(version "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPComp" version))
|
||
(sha256
|
||
(base32
|
||
"1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
|
||
(properties `((upstream-name . "ChIPComp")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
|
||
("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-limma" ,r-limma)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/ChIPComp")
|
||
(synopsis "Quantitative comparison of multiple ChIP-seq datasets")
|
||
(description
|
||
"ChIPComp implements a statistical method for quantitative comparison of
|
||
multiple ChIP-seq datasets. It detects differentially bound sharp binding
|
||
sites across multiple conditions considering matching control in ChIP-seq
|
||
datasets.")
|
||
;; Any version of the GPL.
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-riboprofiling
|
||
(package
|
||
(name "r-riboprofiling")
|
||
(version "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RiboProfiling" version))
|
||
(sha256
|
||
(base32
|
||
"1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
|
||
(properties `((upstream-name . "RiboProfiling")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-data-table" ,r-data-table)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggbio" ,r-ggbio)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-iranges" ,r-iranges)
|
||
("r-plyr" ,r-plyr)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-sqldf" ,r-sqldf)))
|
||
(home-page "https://bioconductor.org/packages/RiboProfiling/")
|
||
(synopsis "Ribosome profiling data analysis")
|
||
(description "Starting with a BAM file, this package provides the
|
||
necessary functions for quality assessment, read start position recalibration,
|
||
the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
|
||
of count data: pairs, log fold-change, codon frequency and coverage
|
||
assessment, principal component analysis on codon coverage.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-riboseqr
|
||
(package
|
||
(name "r-riboseqr")
|
||
(version "1.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "riboSeqR" version))
|
||
(sha256
|
||
(base32
|
||
"1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
|
||
(properties `((upstream-name . "riboSeqR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-abind" ,r-abind)
|
||
("r-bayseq" ,r-bayseq)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-seqlogo" ,r-seqlogo)))
|
||
(home-page "https://bioconductor.org/packages/riboSeqR/")
|
||
(synopsis "Analysis of sequencing data from ribosome profiling experiments")
|
||
(description
|
||
"This package provides plotting functions, frameshift detection and
|
||
parsing of genetic sequencing data from ribosome profiling experiments.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-interactionset
|
||
(package
|
||
(name "r-interactionset")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "InteractionSet" version))
|
||
(sha256
|
||
(base32
|
||
"0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
|
||
(properties
|
||
`((upstream-name . "InteractionSet")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-matrix" ,r-matrix)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://bioconductor.org/packages/InteractionSet")
|
||
(synopsis "Base classes for storing genomic interaction data")
|
||
(description
|
||
"This packages provides the @code{GInteractions},
|
||
@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
|
||
for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
|
||
experiments.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-genomicinteractions
|
||
(package
|
||
(name "r-genomicinteractions")
|
||
(version "1.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GenomicInteractions" version))
|
||
(sha256
|
||
(base32
|
||
"0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
|
||
(properties
|
||
`((upstream-name . "GenomicInteractions")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-data-table" ,r-data-table)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-gviz" ,r-gviz)
|
||
("r-igraph" ,r-igraph)
|
||
("r-interactionset" ,r-interactionset)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-stringr" ,r-stringr)))
|
||
(home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
|
||
(synopsis "R package for handling genomic interaction data")
|
||
(description
|
||
"This R package provides tools for handling genomic interaction data,
|
||
such as ChIA-PET/Hi-C, annotating genomic features with interaction
|
||
information and producing various plots and statistics.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-ctc
|
||
(package
|
||
(name "r-ctc")
|
||
(version "1.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ctc" version))
|
||
(sha256
|
||
(base32
|
||
"0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs `(("r-amap" ,r-amap)))
|
||
(home-page "https://bioconductor.org/packages/ctc/")
|
||
(synopsis "Cluster and tree conversion")
|
||
(description
|
||
"This package provides tools for exporting and importing classification
|
||
trees and clusters to other programs.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-goseq
|
||
(package
|
||
(name "r-goseq")
|
||
(version "1.34.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "goseq" version))
|
||
(sha256
|
||
(base32
|
||
"1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biasedurn" ,r-biasedurn)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-genelendatabase" ,r-genelendatabase)
|
||
("r-go-db" ,r-go-db)
|
||
("r-mgcv" ,r-mgcv)))
|
||
(home-page "https://bioconductor.org/packages/goseq/")
|
||
(synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
|
||
(description
|
||
"This package provides tools to detect Gene Ontology and/or other user
|
||
defined categories which are over/under represented in RNA-seq data.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-glimma
|
||
(package
|
||
(name "r-glimma")
|
||
(version "1.10.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Glimma" version))
|
||
(sha256
|
||
(base32
|
||
"1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
|
||
(properties `((upstream-name . "Glimma")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-edger" ,r-edger)
|
||
("r-jsonlite" ,r-jsonlite)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://github.com/Shians/Glimma")
|
||
(synopsis "Interactive HTML graphics")
|
||
(description
|
||
"This package generates interactive visualisations for analysis of
|
||
RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
|
||
HTML page. The interactions are built on top of the popular static
|
||
representations of analysis results in order to provide additional
|
||
information.")
|
||
(license license:lgpl3)))
|
||
|
||
(define-public r-rots
|
||
(package
|
||
(name "r-rots")
|
||
(version "1.10.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ROTS" version))
|
||
(sha256
|
||
(base32
|
||
"1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
|
||
(properties `((upstream-name . "ROTS")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-rcpp" ,r-rcpp)))
|
||
(home-page "https://bioconductor.org/packages/ROTS/")
|
||
(synopsis "Reproducibility-Optimized Test Statistic")
|
||
(description
|
||
"This package provides tools for calculating the
|
||
@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
|
||
in omics data.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-plgem
|
||
(package
|
||
(name "r-plgem")
|
||
(version "1.54.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "plgem" version))
|
||
(sha256
|
||
(base32
|
||
"1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-mass" ,r-mass)))
|
||
(home-page "http://www.genopolis.it")
|
||
(synopsis "Detect differential expression in microarray and proteomics datasets")
|
||
(description
|
||
"The Power Law Global Error Model (PLGEM) has been shown to faithfully
|
||
model the variance-versus-mean dependence that exists in a variety of
|
||
genome-wide datasets, including microarray and proteomics data. The use of
|
||
PLGEM has been shown to improve the detection of differentially expressed
|
||
genes or proteins in these datasets.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-inspect
|
||
(package
|
||
(name "r-inspect")
|
||
(version "1.12.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "INSPEcT" version))
|
||
(sha256
|
||
(base32
|
||
"07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
|
||
(properties `((upstream-name . "INSPEcT")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-deseq2" ,r-deseq2)
|
||
("r-desolve" ,r-desolve)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-plgem" ,r-plgem)
|
||
("r-preprocesscore" ,r-preprocesscore)
|
||
("r-proc" ,r-proc)
|
||
("r-rootsolve" ,r-rootsolve)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-shiny" ,r-shiny)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-txdb-mmusculus-ucsc-mm9-knowngene"
|
||
,r-txdb-mmusculus-ucsc-mm9-knowngene)))
|
||
(home-page "https://bioconductor.org/packages/INSPEcT")
|
||
(synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
|
||
(description
|
||
"INSPEcT (INference of Synthesis, Processing and dEgradation rates in
|
||
Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
|
||
order to evaluate synthesis, processing and degradation rates and assess via
|
||
modeling the rates that determines changes in mature mRNA levels.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-dnabarcodes
|
||
(package
|
||
(name "r-dnabarcodes")
|
||
(version "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DNABarcodes" version))
|
||
(sha256
|
||
(base32
|
||
"0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
|
||
(properties `((upstream-name . "DNABarcodes")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-bh" ,r-bh)
|
||
("r-matrix" ,r-matrix)
|
||
("r-rcpp" ,r-rcpp)))
|
||
(home-page "https://bioconductor.org/packages/DNABarcodes")
|
||
(synopsis "Create and analyze DNA barcodes")
|
||
(description
|
||
"This package offers tools to create DNA barcode sets capable of
|
||
correcting insertion, deletion, and substitution errors. Existing barcodes
|
||
can be analyzed regarding their minimal, maximal and average distances between
|
||
barcodes. Finally, reads that start with a (possibly mutated) barcode can be
|
||
demultiplexed, i.e. assigned to their original reference barcode.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-ruvseq
|
||
(package
|
||
(name "r-ruvseq")
|
||
(version "1.16.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RUVSeq" version))
|
||
(sha256
|
||
(base32
|
||
"0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
|
||
(properties `((upstream-name . "RUVSeq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-edaseq" ,r-edaseq)
|
||
("r-edger" ,r-edger)
|
||
("r-mass" ,r-mass)))
|
||
(home-page "https://github.com/drisso/RUVSeq")
|
||
(synopsis "Remove unwanted variation from RNA-Seq data")
|
||
(description
|
||
"This package implements methods to @dfn{remove unwanted variation} (RUV)
|
||
of Risso et al. (2014) for the normalization of RNA-Seq read counts between
|
||
samples.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-biocneighbors
|
||
(package
|
||
(name "r-biocneighbors")
|
||
(version "1.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "BiocNeighbors" version))
|
||
(sha256
|
||
(base32
|
||
"1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
|
||
(properties `((upstream-name . "BiocNeighbors")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocparallel" ,r-biocparallel)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rcppannoy" ,r-rcppannoy)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/BiocNeighbors")
|
||
(synopsis "Nearest Neighbor Detection for Bioconductor packages")
|
||
(description
|
||
"This package implements exact and approximate methods for nearest
|
||
neighbor detection, in a framework that allows them to be easily switched
|
||
within Bioconductor packages or workflows. The exact algorithm is implemented
|
||
using pre-clustering with the k-means algorithm. Functions are also provided
|
||
to search for all neighbors within a given distance. Parallelization is
|
||
achieved for all methods using the BiocParallel framework.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-destiny
|
||
(package
|
||
(name "r-destiny")
|
||
(version "2.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "destiny" version))
|
||
(sha256
|
||
(base32
|
||
"1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-fnn" ,r-fnn)
|
||
("r-ggthemes" ,r-ggthemes)
|
||
("r-hmisc" ,r-hmisc)
|
||
("r-igraph" ,r-igraph)
|
||
("r-matrix" ,r-matrix)
|
||
("r-proxy" ,r-proxy)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rcppeigen" ,r-rcppeigen)
|
||
("r-scales" ,r-scales)
|
||
("r-scatterplot3d" ,r-scatterplot3d)
|
||
("r-smoother" ,r-smoother)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-vim" ,r-vim)))
|
||
(home-page "https://bioconductor.org/packages/destiny/")
|
||
(synopsis "Create and plot diffusion maps")
|
||
(description "This package provides tools to create and plot diffusion
|
||
maps.")
|
||
;; Any version of the GPL
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-savr
|
||
(package
|
||
(name "r-savr")
|
||
(version "1.20.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "savR" version))
|
||
(sha256
|
||
(base32
|
||
"13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
|
||
(properties `((upstream-name . "savR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-ggplot2" ,r-ggplot2)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-scales" ,r-scales)
|
||
("r-xml" ,r-xml)))
|
||
(home-page "https://github.com/bcalder/savR")
|
||
(synopsis "Parse and analyze Illumina SAV files")
|
||
(description
|
||
"This package provides tools to parse Illumina Sequence Analysis
|
||
Viewer (SAV) files, access data, and generate QC plots.")
|
||
(license license:agpl3+)))
|
||
|
||
(define-public r-chipexoqual
|
||
(package
|
||
(name "r-chipexoqual")
|
||
(version "1.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPexoQual" version))
|
||
(sha256
|
||
(base32
|
||
"1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
|
||
(properties `((upstream-name . "ChIPexoQual")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocparallel" ,r-biocparallel)
|
||
("r-biovizbase" ,r-biovizbase)
|
||
("r-broom" ,r-broom)
|
||
("r-data-table" ,r-data-table)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-hexbin" ,r-hexbin)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||
("r-rmarkdown" ,r-rmarkdown)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-scales" ,r-scales)
|
||
("r-viridis" ,r-viridis)))
|
||
(home-page "https://github.com/keleslab/ChIPexoQual")
|
||
(synopsis "Quality control pipeline for ChIP-exo/nexus data")
|
||
(description
|
||
"This package provides a quality control pipeline for ChIP-exo/nexus
|
||
sequencing data.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-copynumber
|
||
(package
|
||
(name "r-copynumber")
|
||
(version "1.22.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "copynumber" version))
|
||
(sha256
|
||
(base32
|
||
"0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-s4vectors" ,r-s4vectors)
|
||
("r-iranges" ,r-iranges)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-biocgenerics" ,r-biocgenerics)))
|
||
(home-page "https://bioconductor.org/packages/copynumber")
|
||
(synopsis "Segmentation of single- and multi-track copy number data")
|
||
(description
|
||
"This package segments single- and multi-track copy number data by a
|
||
penalized least squares regression method.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-dnacopy
|
||
(package
|
||
(name "r-dnacopy")
|
||
(version "1.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DNAcopy" version))
|
||
(sha256
|
||
(base32
|
||
"04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
|
||
(properties `((upstream-name . "DNAcopy")))
|
||
(build-system r-build-system)
|
||
(native-inputs `(("gfortran" ,gfortran)))
|
||
(home-page "https://bioconductor.org/packages/DNAcopy")
|
||
(synopsis "DNA copy number data analysis")
|
||
(description
|
||
"This package implements the @dfn{circular binary segmentation} (CBS)
|
||
algorithm to segment DNA copy number data and identify genomic regions with
|
||
abnormal copy number.")
|
||
(license license:gpl2+)))
|
||
|
||
;; This is a CRAN package, but it uncharacteristically depends on a
|
||
;; Bioconductor package.
|
||
(define-public r-htscluster
|
||
(package
|
||
(name "r-htscluster")
|
||
(version "2.0.8")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "HTSCluster" version))
|
||
(sha256
|
||
(base32
|
||
"0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
|
||
(properties `((upstream-name . "HTSCluster")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-capushe" ,r-capushe)
|
||
("r-edger" ,r-edger)
|
||
("r-plotrix" ,r-plotrix)))
|
||
(home-page "https://cran.r-project.org/web/packages/HTSCluster")
|
||
(synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
|
||
(description
|
||
"This package provides a Poisson mixture model is implemented to cluster
|
||
genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
|
||
estimation is performed using either the EM or CEM algorithm, and the slope
|
||
heuristics are used for model selection (i.e., to choose the number of
|
||
clusters).")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-deds
|
||
(package
|
||
(name "r-deds")
|
||
(version "1.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DEDS" version))
|
||
(sha256
|
||
(base32
|
||
"1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
|
||
(properties `((upstream-name . "DEDS")))
|
||
(build-system r-build-system)
|
||
(home-page "https://bioconductor.org/packages/DEDS/")
|
||
(synopsis "Differential expression via distance summary for microarray data")
|
||
(description
|
||
"This library contains functions that calculate various statistics of
|
||
differential expression for microarray data, including t statistics, fold
|
||
change, F statistics, SAM, moderated t and F statistics and B statistics. It
|
||
also implements a new methodology called DEDS (Differential Expression via
|
||
Distance Summary), which selects differentially expressed genes by integrating
|
||
and summarizing a set of statistics using a weighted distance approach.")
|
||
;; Any version of the LGPL.
|
||
(license license:lgpl3+)))
|
||
|
||
;; This is a CRAN package, but since it depends on a Bioconductor package we
|
||
;; put it here.
|
||
(define-public r-nbpseq
|
||
(package
|
||
(name "r-nbpseq")
|
||
(version "0.3.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "NBPSeq" version))
|
||
(sha256
|
||
(base32
|
||
"0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
|
||
(properties `((upstream-name . "NBPSeq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-qvalue" ,r-qvalue)))
|
||
(home-page "https://cran.r-project.org/web/packages/NBPSeq")
|
||
(synopsis "Negative binomial models for RNA-Seq data")
|
||
(description
|
||
"This package provides negative binomial models for two-group comparisons
|
||
and regression inferences from RNA-sequencing data.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-ebseq
|
||
(package
|
||
(name "r-ebseq")
|
||
(version "1.22.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "EBSeq" version))
|
||
(sha256
|
||
(base32
|
||
"1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
|
||
(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-lpsymphony
|
||
(package
|
||
(name "r-lpsymphony")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "lpsymphony" version))
|
||
(sha256
|
||
(base32
|
||
"0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
`(("gfortran" ,gfortran)
|
||
("zlib" ,zlib)))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)))
|
||
(home-page "http://r-forge.r-project.org/projects/rsymphony")
|
||
(synopsis "Symphony integer linear programming solver in R")
|
||
(description
|
||
"This package was derived from Rsymphony. The package provides an R
|
||
interface to SYMPHONY, a linear programming solver written in C++. The main
|
||
difference between this package and Rsymphony is that it includes the solver
|
||
source code, while Rsymphony expects to find header and library files on the
|
||
users' system. Thus the intention of @code{lpsymphony} is to provide an easy
|
||
to install interface to SYMPHONY.")
|
||
;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
|
||
;; lpsimphony is released under the same terms.
|
||
(license license:epl1.0)))
|
||
|
||
(define-public r-ihw
|
||
(package
|
||
(name "r-ihw")
|
||
(version "1.10.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "IHW" version))
|
||
(sha256
|
||
(base32
|
||
"10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
|
||
(properties `((upstream-name . "IHW")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-fdrtool" ,r-fdrtool)
|
||
("r-lpsymphony" ,r-lpsymphony)
|
||
("r-slam" ,r-slam)))
|
||
(home-page "https://bioconductor.org/packages/IHW")
|
||
(synopsis "Independent hypothesis weighting")
|
||
(description
|
||
"@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
|
||
procedure that increases power compared to the method of Benjamini and
|
||
Hochberg by assigning data-driven weights to each hypothesis. The input to
|
||
IHW is a two-column table of p-values and covariates. The covariate can be
|
||
any continuous-valued or categorical variable that is thought to be
|
||
informative on the statistical properties of each hypothesis test, while it is
|
||
independent of the p-value under the null hypothesis.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-icobra
|
||
(package
|
||
(name "r-icobra")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "iCOBRA" version))
|
||
(sha256
|
||
(base32
|
||
"0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"))))
|
||
(properties `((upstream-name . "iCOBRA")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-dplyr" ,r-dplyr)
|
||
("r-dt" ,r-dt)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-limma" ,r-limma)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-rocr" ,r-rocr)
|
||
("r-scales" ,r-scales)
|
||
("r-shiny" ,r-shiny)
|
||
("r-shinybs" ,r-shinybs)
|
||
("r-shinydashboard" ,r-shinydashboard)
|
||
("r-upsetr" ,r-upsetr)))
|
||
(home-page "https://bioconductor.org/packages/iCOBRA")
|
||
(synopsis "Comparison and visualization of ranking and assignment methods")
|
||
(description
|
||
"This package provides functions for calculation and visualization of
|
||
performance metrics for evaluation of ranking and binary
|
||
classification (assignment) methods. It also contains a Shiny application for
|
||
interactive exploration of results.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-mast
|
||
(package
|
||
(name "r-mast")
|
||
(version "1.8.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "MAST" version))
|
||
(sha256
|
||
(base32
|
||
"0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"))))
|
||
(properties `((upstream-name . "MAST")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-abind" ,r-abind)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-data-table" ,r-data-table)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-plyr" ,r-plyr)
|
||
("r-progress" ,r-progress)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-singlecellexperiment" ,r-singlecellexperiment)
|
||
("r-stringr" ,r-stringr)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://github.com/RGLab/MAST/")
|
||
(synopsis "Model-based analysis of single cell transcriptomics")
|
||
(description
|
||
"This package provides methods and models for handling zero-inflated
|
||
single cell assay data.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-monocle
|
||
(package
|
||
(name "r-monocle")
|
||
(version "2.10.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "monocle" version))
|
||
(sha256
|
||
(base32
|
||
"0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocviews" ,r-biocviews)
|
||
("r-cluster" ,r-cluster)
|
||
("r-combinat" ,r-combinat)
|
||
("r-ddrtree" ,r-ddrtree)
|
||
("r-densityclust" ,r-densityclust)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-fastica" ,r-fastica)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-hsmmsinglecell" ,r-hsmmsinglecell)
|
||
("r-igraph" ,r-igraph)
|
||
("r-irlba" ,r-irlba)
|
||
("r-limma" ,r-limma)
|
||
("r-mass" ,r-mass)
|
||
("r-matrix" ,r-matrix)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-pheatmap" ,r-pheatmap)
|
||
("r-plyr" ,r-plyr)
|
||
("r-proxy" ,r-proxy)
|
||
("r-qlcmatrix" ,r-qlcmatrix)
|
||
("r-rann" ,r-rann)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-rtsne" ,r-rtsne)
|
||
("r-slam" ,r-slam)
|
||
("r-stringr" ,r-stringr)
|
||
("r-tibble" ,r-tibble)
|
||
("r-vgam" ,r-vgam)
|
||
("r-viridis" ,r-viridis)))
|
||
(home-page "https://bioconductor.org/packages/monocle")
|
||
(synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
|
||
(description
|
||
"Monocle performs differential expression and time-series analysis for
|
||
single-cell expression experiments. It orders individual cells according to
|
||
progress through a biological process, without knowing ahead of time which
|
||
genes define progress through that process. Monocle also performs
|
||
differential expression analysis, clustering, visualization, and other useful
|
||
tasks on single cell expression data. It is designed to work with RNA-Seq and
|
||
qPCR data, but could be used with other types as well.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-noiseq
|
||
(package
|
||
(name "r-noiseq")
|
||
(version "2.26.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "NOISeq" version))
|
||
(sha256
|
||
(base32
|
||
"1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"))))
|
||
(properties `((upstream-name . "NOISeq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-matrix" ,r-matrix)))
|
||
(home-page "https://bioconductor.org/packages/NOISeq")
|
||
(synopsis "Exploratory analysis and differential expression for RNA-seq data")
|
||
(description
|
||
"This package provides tools to support the analysis of RNA-seq
|
||
expression data or other similar kind of data. It provides exploratory plots
|
||
to evaluate saturation, count distribution, expression per chromosome, type of
|
||
detected features, features length, etc. It also supports the analysis of
|
||
differential expression between two experimental conditions with no parametric
|
||
assumptions.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-scdd
|
||
(package
|
||
(name "r-scdd")
|
||
(version "1.6.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "scDD" version))
|
||
(sha256
|
||
(base32
|
||
"0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"))))
|
||
(properties `((upstream-name . "scDD")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-arm" ,r-arm)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-ebseq" ,r-ebseq)
|
||
("r-fields" ,r-fields)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-mclust" ,r-mclust)
|
||
("r-outliers" ,r-outliers)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-scran" ,r-scran)
|
||
("r-singlecellexperiment" ,r-singlecellexperiment)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://github.com/kdkorthauer/scDD")
|
||
(synopsis "Mixture modeling of single-cell RNA-seq data")
|
||
(description
|
||
"This package implements a method to analyze single-cell RNA-seq data
|
||
utilizing flexible Dirichlet Process mixture models. Genes with differential
|
||
distributions of expression are classified into several interesting patterns
|
||
of differences between two conditions. The package also includes functions
|
||
for simulating data with these patterns from negative binomial
|
||
distributions.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-scone
|
||
(package
|
||
(name "r-scone")
|
||
(version "1.6.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "scone" version))
|
||
(sha256
|
||
(base32
|
||
"0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-aroma-light" ,r-aroma-light)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-boot" ,r-boot)
|
||
("r-class" ,r-class)
|
||
("r-cluster" ,r-cluster)
|
||
("r-compositions" ,r-compositions)
|
||
("r-diptest" ,r-diptest)
|
||
("r-edger" ,r-edger)
|
||
("r-fpc" ,r-fpc)
|
||
("r-gplots" ,r-gplots)
|
||
("r-hexbin" ,r-hexbin)
|
||
("r-limma" ,r-limma)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-mixtools" ,r-mixtools)
|
||
("r-rarpack" ,r-rarpack)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||
("r-rhdf5" ,r-rhdf5)
|
||
("r-ruvseq" ,r-ruvseq)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://bioconductor.org/packages/scone")
|
||
(synopsis "Single cell overview of normalized expression data")
|
||
(description
|
||
"SCONE is an R package for comparing and ranking the performance of
|
||
different normalization schemes for single-cell RNA-seq and other
|
||
high-throughput analyses.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-geoquery
|
||
(package
|
||
(name "r-geoquery")
|
||
(version "2.50.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GEOquery" version))
|
||
(sha256
|
||
(base32
|
||
"074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"))))
|
||
(properties `((upstream-name . "GEOquery")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-httr" ,r-httr)
|
||
("r-limma" ,r-limma)
|
||
("r-magrittr" ,r-magrittr)
|
||
("r-readr" ,r-readr)
|
||
("r-tidyr" ,r-tidyr)
|
||
("r-xml2" ,r-xml2)))
|
||
(home-page "https://github.com/seandavi/GEOquery/")
|
||
(synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
|
||
(description
|
||
"The NCBI Gene Expression Omnibus (GEO) is a public repository of
|
||
microarray data. Given the rich and varied nature of this resource, it is
|
||
only natural to want to apply BioConductor tools to these data. GEOquery is
|
||
the bridge between GEO and BioConductor.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-illuminaio
|
||
(package
|
||
(name "r-illuminaio")
|
||
(version "0.24.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "illuminaio" version))
|
||
(sha256
|
||
(base32
|
||
"1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-base64" ,r-base64)))
|
||
(home-page "https://github.com/HenrikBengtsson/illuminaio/")
|
||
(synopsis "Parse Illumina microarray output files")
|
||
(description
|
||
"This package provides tools for parsing Illumina's microarray output
|
||
files, including IDAT.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-siggenes
|
||
(package
|
||
(name "r-siggenes")
|
||
(version "1.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "siggenes" version))
|
||
(sha256
|
||
(base32
|
||
"0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-multtest" ,r-multtest)))
|
||
(home-page "https://bioconductor.org/packages/siggenes/")
|
||
(synopsis
|
||
"Multiple testing using SAM and Efron's empirical Bayes approaches")
|
||
(description
|
||
"This package provides tools for the identification of differentially
|
||
expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
|
||
both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
|
||
Bayes Analyses of Microarrays} (EBAM).")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-bumphunter
|
||
(package
|
||
(name "r-bumphunter")
|
||
(version "1.24.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "bumphunter" version))
|
||
(sha256
|
||
(base32
|
||
"1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-dorng" ,r-dorng)
|
||
("r-foreach" ,r-foreach)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-iterators" ,r-iterators)
|
||
("r-limma" ,r-limma)
|
||
("r-locfit" ,r-locfit)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://github.com/ririzarr/bumphunter")
|
||
(synopsis "Find bumps in genomic data")
|
||
(description
|
||
"This package provides tools for finding bumps in genomic data in order
|
||
to identify differentially methylated regions in epigenetic epidemiology
|
||
studies.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-minfi
|
||
(package
|
||
(name "r-minfi")
|
||
(version "1.28.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "minfi" version))
|
||
(sha256
|
||
(base32
|
||
"1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-beanplot" ,r-beanplot)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-bumphunter" ,r-bumphunter)
|
||
("r-data-table" ,r-data-table)
|
||
("r-delayedarray" ,r-delayedarray)
|
||
("r-delayedmatrixstats" ,r-delayedmatrixstats)
|
||
("r-genefilter" ,r-genefilter)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-geoquery" ,r-geoquery)
|
||
("r-hdf5array" ,r-hdf5array)
|
||
("r-illuminaio" ,r-illuminaio)
|
||
("r-iranges" ,r-iranges)
|
||
("r-lattice" ,r-lattice)
|
||
("r-limma" ,r-limma)
|
||
("r-mass" ,r-mass)
|
||
("r-mclust" ,r-mclust)
|
||
("r-nlme" ,r-nlme)
|
||
("r-nor1mix" ,r-nor1mix)
|
||
("r-preprocesscore" ,r-preprocesscore)
|
||
("r-quadprog" ,r-quadprog)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||
("r-reshape" ,r-reshape)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-siggenes" ,r-siggenes)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://github.com/hansenlab/minfi")
|
||
(synopsis "Analyze Illumina Infinium DNA methylation arrays")
|
||
(description
|
||
"This package provides tools to analyze and visualize Illumina Infinium
|
||
methylation arrays.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-methylumi
|
||
(package
|
||
(name "r-methylumi")
|
||
(version "2.28.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "methylumi" version))
|
||
(sha256
|
||
(base32
|
||
"14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotate" ,r-annotate)
|
||
("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
|
||
("r-genefilter" ,r-genefilter)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-illuminaio" ,r-illuminaio)
|
||
("r-iranges" ,r-iranges)
|
||
("r-lattice" ,r-lattice)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-minfi" ,r-minfi)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-scales" ,r-scales)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://bioconductor.org/packages/methylumi")
|
||
(synopsis "Handle Illumina methylation data")
|
||
(description
|
||
"This package provides classes for holding and manipulating Illumina
|
||
methylation data. Based on eSet, it can contain MIAME information, sample
|
||
information, feature information, and multiple matrices of data. An
|
||
\"intelligent\" import function, methylumiR can read the Illumina text files
|
||
and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
|
||
HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
|
||
background correction, and quality control features for GoldenGate, Infinium,
|
||
and Infinium HD arrays are also included.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-lumi
|
||
(package
|
||
(name "r-lumi")
|
||
(version "2.34.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "lumi" version))
|
||
(sha256
|
||
(base32
|
||
"1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-affy" ,r-affy)
|
||
("r-annotate" ,r-annotate)
|
||
("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-dbi" ,r-dbi)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-kernsmooth" ,r-kernsmooth)
|
||
("r-lattice" ,r-lattice)
|
||
("r-mass" ,r-mass)
|
||
("r-methylumi" ,r-methylumi)
|
||
("r-mgcv" ,r-mgcv)
|
||
("r-nleqslv" ,r-nleqslv)
|
||
("r-preprocesscore" ,r-preprocesscore)
|
||
("r-rsqlite" ,r-rsqlite)))
|
||
(home-page "https://bioconductor.org/packages/lumi")
|
||
(synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
|
||
(description
|
||
"The lumi package provides an integrated solution for the Illumina
|
||
microarray data analysis. It includes functions of Illumina
|
||
BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
|
||
variance stabilization, normalization and gene annotation at the probe level.
|
||
It also includes the functions of processing Illumina methylation microarrays,
|
||
especially Illumina Infinium methylation microarrays.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-linnorm
|
||
(package
|
||
(name "r-linnorm")
|
||
(version "2.6.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Linnorm" version))
|
||
(sha256
|
||
(base32
|
||
"1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"))))
|
||
(properties `((upstream-name . "Linnorm")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-amap" ,r-amap)
|
||
("r-apcluster" ,r-apcluster)
|
||
("r-ellipse" ,r-ellipse)
|
||
("r-fastcluster" ,r-fastcluster)
|
||
("r-fpc" ,r-fpc)
|
||
("r-ggdendro" ,r-ggdendro)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gmodels" ,r-gmodels)
|
||
("r-igraph" ,r-igraph)
|
||
("r-limma" ,r-limma)
|
||
("r-mass" ,r-mass)
|
||
("r-mclust" ,r-mclust)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rcpparmadillo" ,r-rcpparmadillo)
|
||
("r-rtsne" ,r-rtsne)
|
||
("r-statmod" ,r-statmod)
|
||
("r-vegan" ,r-vegan)
|
||
("r-zoo" ,r-zoo)))
|
||
(home-page "http://www.jjwanglab.org/Linnorm/")
|
||
(synopsis "Linear model and normality based transformation method")
|
||
(description
|
||
"Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
|
||
count data or any large scale count data. It transforms such datasets for
|
||
parametric tests. In addition to the transformtion function (@code{Linnorm}),
|
||
the following pipelines are implemented:
|
||
|
||
@enumerate
|
||
@item Library size/batch effect normalization (@code{Linnorm.Norm})
|
||
@item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
|
||
clustering or hierarchical clustering (@code{Linnorm.tSNE},
|
||
@code{Linnorm.PCA}, @code{Linnorm.HClust})
|
||
@item Differential expression analysis or differential peak detection using
|
||
limma (@code{Linnorm.limma})
|
||
@item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
|
||
@item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
|
||
@item Stable gene selection for scRNA-seq data; for users without or who do
|
||
not want to rely on spike-in genes (@code{Linnorm.SGenes})
|
||
@item Data imputation (@code{Linnorm.DataImput}).
|
||
@end enumerate
|
||
|
||
Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
|
||
@code{RnaXSim} function is included for simulating RNA-seq data for the
|
||
evaluation of DEG analysis methods.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-ioniser
|
||
(package
|
||
(name "r-ioniser")
|
||
(version "2.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "IONiseR" version))
|
||
(sha256
|
||
(base32
|
||
"01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"))))
|
||
(properties `((upstream-name . "IONiseR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-bit64" ,r-bit64)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-magrittr" ,r-magrittr)
|
||
("r-rhdf5" ,r-rhdf5)
|
||
("r-shortread" ,r-shortread)
|
||
("r-stringr" ,r-stringr)
|
||
("r-tibble" ,r-tibble)
|
||
("r-tidyr" ,r-tidyr)
|
||
("r-xvector" ,r-xvector)))
|
||
(home-page "https://bioconductor.org/packages/IONiseR/")
|
||
(synopsis "Quality assessment tools for Oxford Nanopore MinION data")
|
||
(description
|
||
"IONiseR provides tools for the quality assessment of Oxford Nanopore
|
||
MinION data. It extracts summary statistics from a set of fast5 files and can
|
||
be used either before or after base calling. In addition to standard
|
||
summaries of the read-types produced, it provides a number of plots for
|
||
visualising metrics relative to experiment run time or spatially over the
|
||
surface of a flowcell.")
|
||
(license license:expat)))
|
||
|
||
;; This is a CRAN package, but it depends on packages from Bioconductor.
|
||
(define-public r-gkmsvm
|
||
(package
|
||
(name "r-gkmsvm")
|
||
(version "0.79.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "gkmSVM" version))
|
||
(sha256
|
||
(base32
|
||
"04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
|
||
(properties `((upstream-name . "gkmSVM")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-kernlab" ,r-kernlab)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rocr" ,r-rocr)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-seqinr" ,r-seqinr)))
|
||
(home-page "https://cran.r-project.org/web/packages/gkmSVM")
|
||
(synopsis "Gapped-kmer support vector machine")
|
||
(description
|
||
"This R package provides tools for training gapped-kmer SVM classifiers
|
||
for DNA and protein sequences. This package supports several sequence
|
||
kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-triform
|
||
(package
|
||
(name "r-triform")
|
||
(version "1.24.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "triform" version))
|
||
(sha256
|
||
(base32
|
||
"12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-iranges" ,r-iranges)
|
||
("r-yaml" ,r-yaml)))
|
||
(home-page "https://bioconductor.org/packages/triform/")
|
||
(synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
|
||
(description
|
||
"The Triform algorithm uses model-free statistics to identify peak-like
|
||
distributions of TF ChIP sequencing reads, taking advantage of an improved
|
||
peak definition in combination with known profile characteristics.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-varianttools
|
||
(package
|
||
(name "r-varianttools")
|
||
(version "1.24.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "VariantTools" version))
|
||
(sha256
|
||
(base32
|
||
"1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
|
||
(properties `((upstream-name . "VariantTools")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-matrix" ,r-matrix)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-variantannotation" ,r-variantannotation)))
|
||
(home-page "https://bioconductor.org/packages/VariantTools/")
|
||
(synopsis "Tools for exploratory analysis of variant calls")
|
||
(description
|
||
"Explore, diagnose, and compare variant calls using filters. The
|
||
VariantTools package supports a workflow for loading data, calling single
|
||
sample variants and tumor-specific somatic mutations or other sample-specific
|
||
variant types (e.g., RNA editing). Most of the functions operate on
|
||
alignments (BAM files) or datasets of called variants. The user is expected
|
||
to have already aligned the reads with a separate tool, e.g., GSNAP via
|
||
gmapR.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-heatplus
|
||
(package
|
||
(name "r-heatplus")
|
||
(version "2.28.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Heatplus" version))
|
||
(sha256
|
||
(base32
|
||
"0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48"))))
|
||
(properties `((upstream-name . "Heatplus")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-rcolorbrewer" ,r-rcolorbrewer)))
|
||
(home-page "https://github.com/alexploner/Heatplus")
|
||
(synopsis "Heatmaps with row and/or column covariates and colored clusters")
|
||
(description
|
||
"This package provides tools to display a rectangular heatmap (intensity
|
||
plot) of a data matrix. By default, both samples (columns) and features (row)
|
||
of the matrix are sorted according to a hierarchical clustering, and the
|
||
corresponding dendrogram is plotted. Optionally, panels with additional
|
||
information about samples and features can be added to the plot.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-gosemsim
|
||
(package
|
||
(name "r-gosemsim")
|
||
(version "2.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GOSemSim" version))
|
||
(sha256
|
||
(base32
|
||
"0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib"))))
|
||
(properties `((upstream-name . "GOSemSim")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-go-db" ,r-go-db)
|
||
("r-rcpp" ,r-rcpp)))
|
||
(home-page "https://guangchuangyu.github.io/software/GOSemSim")
|
||
(synopsis "GO-terms semantic similarity measures")
|
||
(description
|
||
"The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
|
||
quantitative ways to compute similarities between genes and gene groups, and
|
||
have became important basis for many bioinformatics analysis approaches.
|
||
GOSemSim is an R package for semantic similarity computation among GO terms,
|
||
sets of GO terms, gene products and gene clusters.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-anota
|
||
(package
|
||
(name "r-anota")
|
||
(version "1.30.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "anota" version))
|
||
(sha256
|
||
(base32
|
||
"182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-multtest" ,r-multtest)
|
||
("r-qvalue" ,r-qvalue)))
|
||
(home-page "https://bioconductor.org/packages/anota/")
|
||
(synopsis "Analysis of translational activity")
|
||
(description
|
||
"Genome wide studies of translational control is emerging as a tool to
|
||
study verious biological conditions. The output from such analysis is both
|
||
the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
|
||
involved in translation (the actively translating mRNA level) for each mRNA.
|
||
The standard analysis of such data strives towards identifying differential
|
||
translational between two or more sample classes - i.e. differences in
|
||
actively translated mRNA levels that are independent of underlying differences
|
||
in cytosolic mRNA levels. This package allows for such analysis using partial
|
||
variances and the random variance model. As 10s of thousands of mRNAs are
|
||
analyzed in parallell the library performs a number of tests to assure that
|
||
the data set is suitable for such analysis.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-sigpathway
|
||
(package
|
||
(name "r-sigpathway")
|
||
(version "1.50.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "sigPathway" version))
|
||
(sha256
|
||
(base32
|
||
"0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3"))))
|
||
(properties `((upstream-name . "sigPathway")))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
|
||
(synopsis "Pathway analysis")
|
||
(description
|
||
"This package is used to conduct pathway analysis by calculating the NT_k
|
||
and NE_k statistics in a statistical framework for determining whether a
|
||
specified group of genes for a pathway has a coordinated association with a
|
||
phenotype of interest.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-fgsea
|
||
(package
|
||
(name "r-fgsea")
|
||
(version "1.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "fgsea" version))
|
||
(sha256
|
||
(base32
|
||
"0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocparallel" ,r-biocparallel)
|
||
("r-data-table" ,r-data-table)
|
||
("r-fastmatch" ,r-fastmatch)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-matrix" ,r-matrix)
|
||
("r-rcpp" ,r-rcpp)))
|
||
(home-page "https://github.com/ctlab/fgsea/")
|
||
(synopsis "Fast gene set enrichment analysis")
|
||
(description
|
||
"The package implements an algorithm for fast gene set enrichment
|
||
analysis. Using the fast algorithm allows to make more permutations and get
|
||
more fine grained p-values, which allows to use accurate stantard approaches
|
||
to multiple hypothesis correction.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-dose
|
||
(package
|
||
(name "r-dose")
|
||
(version "3.8.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DOSE" version))
|
||
(sha256
|
||
(base32
|
||
"1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa"))))
|
||
(properties `((upstream-name . "DOSE")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-do-db" ,r-do-db)
|
||
("r-fgsea" ,r-fgsea)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gosemsim" ,r-gosemsim)
|
||
("r-qvalue" ,r-qvalue)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://guangchuangyu.github.io/software/DOSE/")
|
||
(synopsis "Disease ontology semantic and enrichment analysis")
|
||
(description
|
||
"This package implements five methods proposed by Resnik, Schlicker,
|
||
Jiang, Lin and Wang, respectively, for measuring semantic similarities among
|
||
@dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
|
||
including hypergeometric model and gene set enrichment analysis are also
|
||
implemented for discovering disease associations of high-throughput biological
|
||
data.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-enrichplot
|
||
(package
|
||
(name "r-enrichplot")
|
||
(version "1.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "enrichplot" version))
|
||
(sha256
|
||
(base32
|
||
"0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-cowplot" ,r-cowplot)
|
||
("r-dose" ,r-dose)
|
||
("r-europepmc" ,r-europepmc)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-ggplotify" ,r-ggplotify)
|
||
("r-ggraph" ,r-ggraph)
|
||
("r-ggridges" ,r-ggridges)
|
||
("r-gosemsim" ,r-gosemsim)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-igraph" ,r-igraph)
|
||
("r-purrr" ,r-purrr)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-upsetr" ,r-upsetr)))
|
||
(home-page "https://github.com/GuangchuangYu/enrichplot")
|
||
(synopsis "Visualization of functional enrichment result")
|
||
(description
|
||
"The enrichplot package implements several visualization methods for
|
||
interpreting functional enrichment results obtained from ORA or GSEA analyses.
|
||
All the visualization methods are developed based on ggplot2 graphics.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-clusterprofiler
|
||
(package
|
||
(name "r-clusterprofiler")
|
||
(version "3.10.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "clusterProfiler" version))
|
||
(sha256
|
||
(base32
|
||
"1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm"))))
|
||
(properties
|
||
`((upstream-name . "clusterProfiler")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-dose" ,r-dose)
|
||
("r-enrichplot" ,r-enrichplot)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-go-db" ,r-go-db)
|
||
("r-gosemsim" ,r-gosemsim)
|
||
("r-magrittr" ,r-magrittr)
|
||
("r-plyr" ,r-plyr)
|
||
("r-qvalue" ,r-qvalue)
|
||
("r-rvcheck" ,r-rvcheck)
|
||
("r-tidyr" ,r-tidyr)))
|
||
(home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
|
||
(synopsis "Analysis and visualization of functional profiles for gene clusters")
|
||
(description
|
||
"This package implements methods to analyze and visualize functional
|
||
profiles (GO and KEGG) of gene and gene clusters.")
|
||
(license license:artistic2.0)))
|