5950 lines
219 KiB
Scheme
5950 lines
219 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, 2019 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 git-download)
|
||
#:use-module (guix build-system r)
|
||
#:use-module (gnu packages)
|
||
#:use-module (gnu packages base)
|
||
#:use-module (gnu packages bioinformatics)
|
||
#:use-module (gnu packages cran)
|
||
#:use-module (gnu packages compression)
|
||
#:use-module (gnu packages gcc)
|
||
#:use-module (gnu packages graph)
|
||
#:use-module (gnu packages haskell-xyz)
|
||
#:use-module (gnu packages image)
|
||
#:use-module (gnu packages maths)
|
||
#:use-module (gnu packages netpbm)
|
||
#:use-module (gnu packages perl)
|
||
#:use-module (gnu packages pkg-config)
|
||
#:use-module (gnu packages statistics)
|
||
#:use-module (gnu packages web)
|
||
#:use-module (srfi srfi-1))
|
||
|
||
|
||
;;; Annotations
|
||
|
||
(define-public r-bsgenome-celegans-ucsc-ce6
|
||
(package
|
||
(name "r-bsgenome-celegans-ucsc-ce6")
|
||
(version "1.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
|
||
version 'annotation))
|
||
(sha256
|
||
(base32
|
||
"0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
|
||
(properties
|
||
`((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-bsgenome" ,r-bsgenome)))
|
||
(home-page
|
||
"https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
|
||
(synopsis "Full genome sequences for Worm")
|
||
(description
|
||
"This package provides full genome sequences for Caenorhabditis
|
||
elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
|
||
objects.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-bsgenome-celegans-ucsc-ce10
|
||
(package
|
||
(name "r-bsgenome-celegans-ucsc-ce10")
|
||
(version "1.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; 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-ensdb-hsapiens-v75
|
||
(package
|
||
(name "r-ensdb-hsapiens-v75")
|
||
(version "2.99.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
|
||
(sha256
|
||
(base32
|
||
"0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
|
||
(properties
|
||
`((upstream-name . "EnsDb.Hsapiens.v75")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-ensembldb" ,r-ensembldb)))
|
||
(home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
|
||
(synopsis "Ensembl based annotation package")
|
||
(description
|
||
"This package exposes an annotation database generated from Ensembl.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-genelendatabase
|
||
(package
|
||
(name "r-genelendatabase")
|
||
(version "1.18.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
;; 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-hsapiens-ucsc-hg38-knowngene
|
||
(package
|
||
(name "r-txdb-hsapiens-ucsc-hg38-knowngene")
|
||
(version "3.4.6")
|
||
(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.hg38.knownGene_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
|
||
(properties
|
||
`((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-genomicfeatures" ,r-genomicfeatures)))
|
||
(home-page
|
||
"https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
|
||
(synopsis "Annotation package for human genome in TxDb format")
|
||
(description
|
||
"This package provides an annotation database of Homo sapiens genome
|
||
data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
|
||
track. The database is exposed as a @code{TxDb} object.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-txdb-mmusculus-ucsc-mm9-knowngene
|
||
(package
|
||
(name "r-txdb-mmusculus-ucsc-mm9-knowngene")
|
||
(version "3.2.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; 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 "3.4.7")
|
||
(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
|
||
"04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
|
||
(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-txdb-celegans-ucsc-ce6-ensgene
|
||
(package
|
||
(name "r-txdb-celegans-ucsc-ce6-ensgene")
|
||
(version "3.2.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
|
||
version 'annotation))
|
||
(sha256
|
||
(base32
|
||
"1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
|
||
(properties
|
||
`((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-genomicfeatures" ,r-genomicfeatures)))
|
||
(home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
|
||
(synopsis "Annotation package for C elegans TxDb objects")
|
||
(description
|
||
"This package exposes a C elegans annotation database generated from UCSC
|
||
by exposing these as TxDb objects.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-fdb-infiniummethylation-hg19
|
||
(package
|
||
(name "r-fdb-infiniummethylation-hg19")
|
||
(version "2.2.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; 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)))
|
||
|
||
(define-public r-pfam-db
|
||
(package
|
||
(name "r-pfam-db")
|
||
(version "3.8.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "PFAM.db" version 'annotation))
|
||
(sha256
|
||
(base32
|
||
"0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
|
||
(properties `((upstream-name . "PFAM.db")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)))
|
||
(home-page "https://bioconductor.org/packages/PFAM.db")
|
||
(synopsis "Set of protein ID mappings for PFAM")
|
||
(description
|
||
"This package provides a set of protein ID mappings for PFAM, assembled
|
||
using data from public repositories.")
|
||
(license license:artistic2.0)))
|
||
|
||
|
||
;;; Experiment data
|
||
|
||
(define-public r-abadata
|
||
(package
|
||
(name "r-abadata")
|
||
(version "1.12.0")
|
||
(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/"
|
||
"ABAData_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
|
||
(properties
|
||
`((upstream-name . "ABAData")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)))
|
||
(home-page "https://www.bioconductor.org/packages/ABAData/")
|
||
(synopsis "Gene expression in human brain regions from Allen Brain Atlas")
|
||
(description
|
||
"This package provides the data for the gene expression enrichment
|
||
analysis conducted in the package ABAEnrichment. The package includes three
|
||
datasets which are derived from the Allen Brain Atlas:
|
||
|
||
@enumerate
|
||
@item Gene expression data from Human Brain (adults) averaged across donors,
|
||
@item Gene expression data from the Developing Human Brain pooled into five
|
||
age categories and averaged across donors, and
|
||
@item a developmental effect score based on the Developing Human Brain
|
||
expression data.
|
||
@end enumerate
|
||
|
||
All datasets are restricted to protein coding genes.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-arrmdata
|
||
(package
|
||
(name "r-arrmdata")
|
||
(version "1.18.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; 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/"
|
||
"ARRmData_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
|
||
(properties
|
||
`((upstream-name . "ARRmData")))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.bioconductor.org/packages/ARRmData/")
|
||
(synopsis "Example dataset for normalization of Illumina 450k methylation data")
|
||
(description
|
||
"This package provides raw beta values from 36 samples across 3 groups
|
||
from Illumina 450k methylation arrays.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-hsmmsinglecell
|
||
(package
|
||
(name "r-hsmmsinglecell")
|
||
(version "1.2.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; 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)))
|
||
|
||
(define-public r-all
|
||
(package
|
||
(name "r-all")
|
||
(version "1.26.0")
|
||
(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/"
|
||
"ALL_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
|
||
(properties `((upstream-name . "ALL")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)))
|
||
(home-page "https://bioconductor.org/packages/ALL")
|
||
(synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
|
||
(description
|
||
"The data consist of microarrays from 128 different individuals with
|
||
@dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
|
||
are available. The data have been normalized (using rma) and it is the
|
||
jointly normalized data that are available here. The data are presented in
|
||
the form of an @code{exprSet} object.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-affydata
|
||
(package
|
||
(name "r-affydata")
|
||
(version "1.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "affydata" version 'experiment))
|
||
(sha256
|
||
(base32
|
||
"1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
|
||
(properties `((upstream-name . "affydata")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-affy" ,r-affy)))
|
||
(home-page "https://bioconductor.org/packages/affydata/")
|
||
(synopsis "Affymetrix data for demonstration purposes")
|
||
(description
|
||
"This package provides example datasets that represent 'real world
|
||
examples' of Affymetrix data, unlike the artificial examples included in the
|
||
package @code{affy}.")
|
||
(license license:gpl2+)))
|
||
|
||
|
||
;;; Packages
|
||
|
||
(define-public r-biocgenerics
|
||
(package
|
||
(name "r-biocgenerics")
|
||
(version "0.30.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "BiocGenerics" version))
|
||
(sha256
|
||
(base32
|
||
"1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
|
||
(properties
|
||
`((upstream-name . "BiocGenerics")))
|
||
(build-system r-build-system)
|
||
(home-page "https://bioconductor.org/packages/BiocGenerics")
|
||
(synopsis "S4 generic functions for Bioconductor")
|
||
(description
|
||
"This package provides S4 generic functions needed by many Bioconductor
|
||
packages.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-affycomp
|
||
(package
|
||
(name "r-affycomp")
|
||
(version "1.60.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "affycomp" version))
|
||
(sha256
|
||
(base32
|
||
"1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n"))))
|
||
(properties `((upstream-name . "affycomp")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs `(("r-biobase" ,r-biobase)))
|
||
(home-page "https://bioconductor.org/packages/affycomp/")
|
||
(synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
|
||
(description
|
||
"The package contains functions that can be used to compare expression
|
||
measures for Affymetrix Oligonucleotide Arrays.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-affycompatible
|
||
(package
|
||
(name "r-affycompatible")
|
||
(version "1.44.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "AffyCompatible" version))
|
||
(sha256
|
||
(base32
|
||
"1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs"))))
|
||
(properties
|
||
`((upstream-name . "AffyCompatible")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biostrings" ,r-biostrings)
|
||
("r-rcurl" ,r-rcurl)
|
||
("r-xml" ,r-xml)))
|
||
(home-page "https://bioconductor.org/packages/AffyCompatible/")
|
||
(synopsis "Work with Affymetrix GeneChip files")
|
||
(description
|
||
"This package provides an interface to Affymetrix chip annotation and
|
||
sample attribute files. The package allows an easy way for users to download
|
||
and manage local data bases of Affynmetrix NetAffx annotation files. It also
|
||
provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
|
||
Command Console} (AGCC)-compatible sample annotation files.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-affycontam
|
||
(package
|
||
(name "r-affycontam")
|
||
(version "1.42.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "affyContam" version))
|
||
(sha256
|
||
(base32
|
||
"0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp"))))
|
||
(properties `((upstream-name . "affyContam")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-affy" ,r-affy)
|
||
("r-affydata" ,r-affydata)
|
||
("r-biobase" ,r-biobase)))
|
||
(home-page "https://bioconductor.org/packages/affyContam/")
|
||
(synopsis "Structured corruption of Affymetrix CEL file data")
|
||
(description
|
||
"Microarray quality assessment is a major concern of microarray analysts.
|
||
This package provides some simple approaches to in silico creation of quality
|
||
problems in CEL-level data to help evaluate performance of quality metrics.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-affycoretools
|
||
(package
|
||
(name "r-affycoretools")
|
||
(version "1.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "affycoretools" version))
|
||
(sha256
|
||
(base32
|
||
"17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s"))))
|
||
(properties `((upstream-name . "affycoretools")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-affy" ,r-affy)
|
||
("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-dbi" ,r-dbi)
|
||
("r-edger" ,r-edger)
|
||
("r-gcrma" ,r-gcrma)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gostats" ,r-gostats)
|
||
("r-gplots" ,r-gplots)
|
||
("r-hwriter" ,r-hwriter)
|
||
("r-lattice" ,r-lattice)
|
||
("r-limma" ,r-limma)
|
||
("r-oligoclasses" ,r-oligoclasses)
|
||
("r-reportingtools" ,r-reportingtools)
|
||
("r-rsqlite" ,r-rsqlite)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-xtable" ,r-xtable)))
|
||
(home-page "https://bioconductor.org/packages/affycoretools/")
|
||
(synopsis "Functions for analyses with Affymetrix GeneChips")
|
||
(description
|
||
"This package provides various wrapper functions that have been written
|
||
to streamline the more common analyses that a Biostatistician might see.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-affxparser
|
||
(package
|
||
(name "r-affxparser")
|
||
(version "1.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "affxparser" version))
|
||
(sha256
|
||
(base32
|
||
"1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33"))))
|
||
(properties `((upstream-name . "affxparser")))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/HenrikBengtsson/affxparser")
|
||
(synopsis "Affymetrix File Parsing SDK")
|
||
(description
|
||
"This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
|
||
BAR). It provides methods for fast and memory efficient parsing of Affymetrix
|
||
files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
|
||
are supported. Currently, there are methods for reading @dfn{chip definition
|
||
file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
|
||
either in full or in part. For example, probe signals from a few probesets
|
||
can be extracted very quickly from a set of CEL files into a convenient list
|
||
structure.")
|
||
;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
|
||
;; under LGPLv2+.
|
||
(license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
|
||
|
||
(define-public r-annotate
|
||
(package
|
||
(name "r-annotate")
|
||
(version "1.62.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "annotate" version))
|
||
(sha256
|
||
(base32
|
||
"0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
|
||
(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 "1.26.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "hpar" version))
|
||
(sha256
|
||
(base32
|
||
"1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
|
||
(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 "1.16.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "regioneR" version))
|
||
(sha256
|
||
(base32
|
||
"0xzk057h6nkr3rvd412prxgnkpq625b90laj1kwb0i5q8j5ch760"))))
|
||
(properties `((upstream-name . "regioneR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biostrings" ,r-biostrings)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-memoise" ,r-memoise)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/regioneR/")
|
||
(synopsis "Association analysis of genomic regions")
|
||
(description "This package offers a statistical framework based on
|
||
customizable permutation tests to assess the association between genomic
|
||
region sets and other genomic features.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-reportingtools
|
||
(package
|
||
(name "r-reportingtools")
|
||
(version "2.24.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ReportingTools" version))
|
||
(sha256
|
||
(base32
|
||
"16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc"))))
|
||
(properties
|
||
`((upstream-name . "ReportingTools")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotate" ,r-annotate)
|
||
("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-category" ,r-category)
|
||
("r-deseq2" ,r-deseq2)
|
||
("r-edger" ,r-edger)
|
||
("r-ggbio" ,r-ggbio)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gostats" ,r-gostats)
|
||
("r-gseabase" ,r-gseabase)
|
||
("r-hwriter" ,r-hwriter)
|
||
("r-iranges" ,r-iranges)
|
||
("r-knitr" ,r-knitr)
|
||
("r-lattice" ,r-lattice)
|
||
("r-limma" ,r-limma)
|
||
("r-pfam-db" ,r-pfam-db)
|
||
("r-r-utils" ,r-r-utils)
|
||
("r-xml" ,r-xml)))
|
||
(home-page "https://bioconductor.org/packages/ReportingTools/")
|
||
(synopsis "Tools for making reports in various formats")
|
||
(description
|
||
"The ReportingTools package enables users to easily display reports of
|
||
analysis results generated from sources such as microarray and sequencing
|
||
data. The package allows users to create HTML pages that may be viewed on a
|
||
web browser, or in other formats. Users can generate tables with sortable and
|
||
filterable columns, make and display plots, and link table entries to other
|
||
data sources such as NCBI or larger plots within the HTML page. Using the
|
||
package, users can also produce a table of contents page to link various
|
||
reports together for a particular project that can be viewed in a web
|
||
browser.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-geneplotter
|
||
(package
|
||
(name "r-geneplotter")
|
||
(version "1.62.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "geneplotter" version))
|
||
(sha256
|
||
(base32
|
||
"0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotate" ,r-annotate)
|
||
("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-lattice" ,r-lattice)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)))
|
||
(home-page "https://bioconductor.org/packages/geneplotter")
|
||
(synopsis "Graphics functions for genomic data")
|
||
(description
|
||
"This package provides functions for plotting genomic data.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-oligoclasses
|
||
(package
|
||
(name "r-oligoclasses")
|
||
(version "1.46.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "oligoClasses" version))
|
||
(sha256
|
||
(base32
|
||
"0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72"))))
|
||
(properties `((upstream-name . "oligoClasses")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-affyio" ,r-affyio)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocmanager" ,r-biocmanager)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-dbi" ,r-dbi)
|
||
("r-ff" ,r-ff)
|
||
("r-foreach" ,r-foreach)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rsqlite" ,r-rsqlite)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://bioconductor.org/packages/oligoClasses/")
|
||
(synopsis "Classes for high-throughput arrays")
|
||
(description
|
||
"This package contains class definitions, validity checks, and
|
||
initialization methods for classes used by the @code{oligo} and @code{crlmm}
|
||
packages.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-oligo
|
||
(package
|
||
(name "r-oligo")
|
||
(version "1.48.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "oligo" version))
|
||
(sha256
|
||
(base32
|
||
"0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df"))))
|
||
(properties `((upstream-name . "oligo")))
|
||
(build-system r-build-system)
|
||
(inputs `(("zlib" ,zlib)))
|
||
(propagated-inputs
|
||
`(("r-affxparser" ,r-affxparser)
|
||
("r-affyio" ,r-affyio)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-dbi" ,r-dbi)
|
||
("r-ff" ,r-ff)
|
||
("r-oligoclasses" ,r-oligoclasses)
|
||
("r-preprocesscore" ,r-preprocesscore)
|
||
("r-rsqlite" ,r-rsqlite)
|
||
("r-zlibbioc" ,r-zlibbioc)))
|
||
(home-page "https://bioconductor.org/packages/oligo/")
|
||
(synopsis "Preprocessing tools for oligonucleotide arrays")
|
||
(description
|
||
"This package provides a package to analyze oligonucleotide
|
||
arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
|
||
Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-qvalue
|
||
(package
|
||
(name "r-qvalue")
|
||
(version "2.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "qvalue" version))
|
||
(sha256
|
||
(base32
|
||
"00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
|
||
(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 "2.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DiffBind" version))
|
||
(sha256
|
||
(base32
|
||
"1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
|
||
(properties `((upstream-name . "DiffBind")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
`(("zlib" ,zlib)))
|
||
(propagated-inputs
|
||
`(("r-amap" ,r-amap)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-deseq2" ,r-deseq2)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-edger" ,r-edger)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-ggrepel" ,r-ggrepel)
|
||
("r-gplots" ,r-gplots)
|
||
("r-iranges" ,r-iranges)
|
||
("r-lattice" ,r-lattice)
|
||
("r-limma" ,r-limma)
|
||
("r-locfit" ,r-locfit)
|
||
("r-rcolorbrewer" , r-rcolorbrewer)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rhtslib" ,r-rhtslib)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-systempiper" ,r-systempiper)))
|
||
(home-page "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 "1.24.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RIPSeeker" version))
|
||
(sha256
|
||
(base32
|
||
"0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
|
||
(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 "2.40.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "multtest" version))
|
||
(sha256
|
||
(base32
|
||
"0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
|
||
(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 "1.62.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "graph" version))
|
||
(sha256
|
||
(base32
|
||
"0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
|
||
(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 "3.18.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPpeakAnno" version))
|
||
(sha256
|
||
(base32
|
||
"0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
|
||
(properties `((upstream-name . "ChIPpeakAnno")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocmanager" ,r-biocmanager)
|
||
("r-biomart" ,r-biomart)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-dbi" ,r-dbi)
|
||
("r-delayedarray" ,r-delayedarray)
|
||
("r-ensembldb" ,r-ensembldb)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-go-db" ,r-go-db)
|
||
("r-graph" ,r-graph)
|
||
("r-idr" ,r-idr)
|
||
("r-iranges" ,r-iranges)
|
||
("r-limma" ,r-limma)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-multtest" ,r-multtest)
|
||
("r-rbgl" ,r-rbgl)
|
||
("r-regioner" ,r-regioner)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-seqinr" ,r-seqinr)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-venndiagram" ,r-venndiagram)))
|
||
(home-page "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 "1.62.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "marray" version))
|
||
(sha256
|
||
(base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
|
||
(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 functions for data input, diagnostic plots,
|
||
normalization and quality checking.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-cghbase
|
||
(package
|
||
(name "r-cghbase")
|
||
(version "1.44.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "CGHbase" version))
|
||
(sha256
|
||
(base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
|
||
(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 "2.46.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "CGHcall" version))
|
||
(sha256
|
||
(base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
|
||
(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 "1.20.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "QDNAseq" version))
|
||
(sha256
|
||
(base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
|
||
(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 "2.18.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "baySeq" version))
|
||
(sha256
|
||
(base32
|
||
"13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
|
||
(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 "1.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPComp" version))
|
||
(sha256
|
||
(base32
|
||
"0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
|
||
(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 "1.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RiboProfiling" version))
|
||
(sha256
|
||
(base32
|
||
"1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
|
||
(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 "1.18.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "riboSeqR" version))
|
||
(sha256
|
||
(base32
|
||
"1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
|
||
(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 "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "InteractionSet" version))
|
||
(sha256
|
||
(base32
|
||
"0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
|
||
(properties
|
||
`((upstream-name . "InteractionSet")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-matrix" ,r-matrix)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://bioconductor.org/packages/InteractionSet")
|
||
(synopsis "Base classes for storing genomic interaction data")
|
||
(description
|
||
"This package provides the @code{GInteractions},
|
||
@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
|
||
for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
|
||
experiments.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-genomicinteractions
|
||
(package
|
||
(name "r-genomicinteractions")
|
||
(version "1.18.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GenomicInteractions" version))
|
||
(sha256
|
||
(base32
|
||
"0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
|
||
(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 "1.58.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ctc" version))
|
||
(sha256
|
||
(base32
|
||
"15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
|
||
(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 "1.36.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "goseq" version))
|
||
(sha256
|
||
(base32
|
||
"0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
|
||
(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 "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Glimma" version))
|
||
(sha256
|
||
(base32
|
||
"11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
|
||
(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 "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ROTS" version))
|
||
(sha256
|
||
(base32
|
||
"1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
|
||
(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 "1.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "plgem" version))
|
||
(sha256
|
||
(base32
|
||
"0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
|
||
(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 "1.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "INSPEcT" version))
|
||
(sha256
|
||
(base32
|
||
"1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
|
||
(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 "1.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DNABarcodes" version))
|
||
(sha256
|
||
(base32
|
||
"1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
|
||
(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 "1.18.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RUVSeq" version))
|
||
(sha256
|
||
(base32
|
||
"0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
|
||
(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 "1.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "BiocNeighbors" version))
|
||
(sha256
|
||
(base32
|
||
"08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
|
||
(properties `((upstream-name . "BiocNeighbors")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rcppannoy" ,r-rcppannoy)
|
||
("r-rcpphnsw" ,r-rcpphnsw)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/BiocNeighbors")
|
||
(synopsis "Nearest Neighbor Detection for Bioconductor packages")
|
||
(description
|
||
"This package implements exact and approximate methods for nearest
|
||
neighbor detection, in a framework that allows them to be easily switched
|
||
within Bioconductor packages or workflows. The exact algorithm is implemented
|
||
using pre-clustering with the k-means algorithm. Functions are also provided
|
||
to search for all neighbors within a given distance. Parallelization is
|
||
achieved for all methods using the BiocParallel framework.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-biocsingular
|
||
(package
|
||
(name "r-biocsingular")
|
||
(version "1.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "BiocSingular" version))
|
||
(sha256
|
||
(base32
|
||
"129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
|
||
(properties `((upstream-name . "BiocSingular")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-beachmat" ,r-beachmat)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-delayedarray" ,r-delayedarray)
|
||
("r-irlba" ,r-irlba)
|
||
("r-matrix" ,r-matrix)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rsvd" ,r-rsvd)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://github.com/LTLA/BiocSingular")
|
||
(synopsis "Singular value decomposition for Bioconductor packages")
|
||
(description
|
||
"This package implements exact and approximate methods for singular value
|
||
decomposition and principal components analysis, in a framework that allows
|
||
them to be easily switched within Bioconductor packages or workflows. Where
|
||
possible, parallelization is achieved using the BiocParallel framework.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-destiny
|
||
(package
|
||
(name "r-destiny")
|
||
(version "2.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "destiny" version))
|
||
(sha256
|
||
(base32
|
||
"1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-ggthemes" ,r-ggthemes)
|
||
("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 "1.22.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "savR" version))
|
||
(sha256
|
||
(base32
|
||
"101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
|
||
(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 "1.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPexoQual" version))
|
||
(sha256
|
||
(base32
|
||
"02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
|
||
(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 "1.24.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "copynumber" version))
|
||
(sha256
|
||
(base32
|
||
"0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
|
||
(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 "1.58.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DNAcopy" version))
|
||
(sha256
|
||
(base32
|
||
"1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
|
||
(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 "1.58.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DEDS" version))
|
||
(sha256
|
||
(base32
|
||
"029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
|
||
(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 "1.24.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "EBSeq" version))
|
||
(sha256
|
||
(base32
|
||
"13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
|
||
(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 "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "lpsymphony" version))
|
||
(sha256
|
||
(base32
|
||
"13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
|
||
(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 "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "IHW" version))
|
||
(sha256
|
||
(base32
|
||
"05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
|
||
(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 "1.12.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "iCOBRA" version))
|
||
(sha256
|
||
(base32
|
||
"1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
|
||
(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 "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "MAST" version))
|
||
(sha256
|
||
(base32
|
||
"0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
|
||
(properties `((upstream-name . "MAST")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-abind" ,r-abind)
|
||
("r-blme" ,r-blme)
|
||
("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 "2.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "monocle" version))
|
||
(sha256
|
||
(base32
|
||
"1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
|
||
(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-monocle3
|
||
(package
|
||
(name "r-monocle3")
|
||
(version "0.1.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/cole-trapnell-lab/monocle3.git")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-delayedmatrixstats" ,r-delayedmatrixstats)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-ggrepel" ,r-ggrepel)
|
||
("r-grr" ,r-grr)
|
||
("r-htmlwidgets" ,r-htmlwidgets)
|
||
("r-igraph" ,r-igraph)
|
||
("r-irlba" ,r-irlba)
|
||
("r-limma" ,r-limma)
|
||
("r-lmtest" ,r-lmtest)
|
||
("r-mass" ,r-mass)
|
||
("r-matrix" ,r-matrix)
|
||
("r-matrix-utils" ,r-matrix-utils)
|
||
("r-pbapply" ,r-pbapply)
|
||
("r-pbmcapply" ,r-pbmcapply)
|
||
("r-pheatmap" ,r-pheatmap)
|
||
("r-plotly" ,r-plotly)
|
||
("r-pryr" ,r-pryr)
|
||
("r-proxy" ,r-proxy)
|
||
("r-pscl" ,r-pscl)
|
||
("r-purrr" ,r-purrr)
|
||
("r-rann" ,r-rann)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rcppparallel" ,r-rcppparallel)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-reticulate" ,r-reticulate)
|
||
("r-rhpcblasctl" ,r-rhpcblasctl)
|
||
("r-rtsne" ,r-rtsne)
|
||
("r-shiny" ,r-shiny)
|
||
("r-slam" ,r-slam)
|
||
("r-spdep" ,r-spdep)
|
||
("r-speedglm" ,r-speedglm)
|
||
("r-stringr" ,r-stringr)
|
||
("r-singlecellexperiment" ,r-singlecellexperiment)
|
||
("r-tibble" ,r-tibble)
|
||
("r-tidyr" ,r-tidyr)
|
||
("r-uwot" ,r-uwot)
|
||
("r-viridis" ,r-viridis)))
|
||
(home-page "https://github.com/cole-trapnell-lab/monocle3")
|
||
(synopsis "Analysis toolkit for single-cell RNA-Seq data")
|
||
(description
|
||
"Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-noiseq
|
||
(package
|
||
(name "r-noiseq")
|
||
(version "2.28.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "NOISeq" version))
|
||
(sha256
|
||
(base32
|
||
"1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
|
||
(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 "1.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "scDD" version))
|
||
(sha256
|
||
(base32
|
||
"01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
|
||
(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 "1.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "scone" version))
|
||
(sha256
|
||
(base32
|
||
"00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
|
||
(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 "2.52.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GEOquery" version))
|
||
(sha256
|
||
(base32
|
||
"1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
|
||
(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 "0.26.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "illuminaio" version))
|
||
(sha256
|
||
(base32
|
||
"18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
|
||
(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 "1.58.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "siggenes" version))
|
||
(sha256
|
||
(base32
|
||
"178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-multtest" ,r-multtest)
|
||
("r-scrime" ,r-scrime)))
|
||
(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 "1.26.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "bumphunter" version))
|
||
(sha256
|
||
(base32
|
||
"1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
|
||
(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 "1.30.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "minfi" version))
|
||
(sha256
|
||
(base32
|
||
"0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
|
||
(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 "2.30.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "methylumi" version))
|
||
(sha256
|
||
(base32
|
||
"13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
|
||
(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 "2.36.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "lumi" version))
|
||
(sha256
|
||
(base32
|
||
"1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
|
||
(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 "2.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Linnorm" version))
|
||
(sha256
|
||
(base32
|
||
"1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
|
||
(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 "2.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "IONiseR" version))
|
||
(sha256
|
||
(base32
|
||
"0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
|
||
(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 "1.26.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "triform" version))
|
||
(sha256
|
||
(base32
|
||
"0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
|
||
(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 "1.26.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "VariantTools" version))
|
||
(sha256
|
||
(base32
|
||
"0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
|
||
(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 "2.30.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Heatplus" version))
|
||
(sha256
|
||
(base32
|
||
"18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
|
||
(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 "2.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GOSemSim" version))
|
||
(sha256
|
||
(base32
|
||
"035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
|
||
(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 "1.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "anota" version))
|
||
(sha256
|
||
(base32
|
||
"0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
|
||
(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 various 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 parallel 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 "1.52.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "sigPathway" version))
|
||
(sha256
|
||
(base32
|
||
"1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
|
||
(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 "1.10.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "fgsea" version))
|
||
(sha256
|
||
(base32
|
||
"1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-bh" ,r-bh)
|
||
("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 "3.10.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DOSE" version))
|
||
(sha256
|
||
(base32
|
||
"06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
|
||
(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 "1.4.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "enrichplot" version))
|
||
(sha256
|
||
(base32
|
||
"1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
|
||
(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 "3.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "clusterProfiler" version))
|
||
(sha256
|
||
(base32
|
||
"1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
|
||
(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)))
|
||
|
||
(define-public r-mlinterfaces
|
||
(package
|
||
(name "r-mlinterfaces")
|
||
(version "1.64.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "MLInterfaces" version))
|
||
(sha256
|
||
(base32
|
||
"0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
|
||
(properties `((upstream-name . "MLInterfaces")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotate" ,r-annotate)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-cluster" ,r-cluster)
|
||
("r-fpc" ,r-fpc)
|
||
("r-gbm" ,r-gbm)
|
||
("r-gdata" ,r-gdata)
|
||
("r-genefilter" ,r-genefilter)
|
||
("r-ggvis" ,r-ggvis)
|
||
("r-hwriter" ,r-hwriter)
|
||
("r-mass" ,r-mass)
|
||
("r-mlbench" ,r-mlbench)
|
||
("r-pls" ,r-pls)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||
("r-rda" ,r-rda)
|
||
("r-rpart" ,r-rpart)
|
||
("r-sfsmisc" ,r-sfsmisc)
|
||
("r-shiny" ,r-shiny)
|
||
("r-threejs" ,r-threejs)))
|
||
(home-page "https://bioconductor.org/packages/MLInterfaces/")
|
||
(synopsis "Interfaces to R machine learning procedures")
|
||
(description
|
||
"This package provides uniform interfaces to machine learning code for
|
||
data in R and Bioconductor containers.")
|
||
;; Any version of the LGPL.
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-annaffy
|
||
(package
|
||
(name "r-annaffy")
|
||
(version "1.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "annaffy" version))
|
||
(sha256
|
||
(base32
|
||
"0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'remove-reference-to-non-free-data
|
||
(lambda _
|
||
(substitute* "DESCRIPTION"
|
||
((", KEGG.db") ""))
|
||
#t)))))
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-dbi" ,r-dbi)
|
||
("r-go-db" ,r-go-db)))
|
||
(home-page "https://bioconductor.org/packages/annaffy/")
|
||
(synopsis "Annotation tools for Affymetrix biological metadata")
|
||
(description
|
||
"This package provides functions for handling data from Bioconductor
|
||
Affymetrix annotation data packages. It produces compact HTML and text
|
||
reports including experimental data and URL links to many online databases.
|
||
It allows searching of biological metadata using various criteria.")
|
||
;; Any version of the LGPL according to the DESCRIPTION file. A copy of
|
||
;; the LGPL 2.1 is included.
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-a4core
|
||
(package
|
||
(name "r-a4core")
|
||
(version "1.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "a4Core" version))
|
||
(sha256
|
||
(base32
|
||
"1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
|
||
(properties `((upstream-name . "a4Core")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-glmnet" ,r-glmnet)))
|
||
(home-page "https://bioconductor.org/packages/a4Core")
|
||
(synopsis "Automated Affymetrix array analysis core package")
|
||
(description
|
||
"This is the core package for the automated analysis of Affymetrix
|
||
arrays.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-a4classif
|
||
(package
|
||
(name "r-a4classif")
|
||
(version "1.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "a4Classif" version))
|
||
(sha256
|
||
(base32
|
||
"1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
|
||
(properties `((upstream-name . "a4Classif")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-a4core" ,r-a4core)
|
||
("r-a4preproc" ,r-a4preproc)
|
||
("r-glmnet" ,r-glmnet)
|
||
("r-mlinterfaces" ,r-mlinterfaces)
|
||
("r-pamr" ,r-pamr)
|
||
("r-rocr" ,r-rocr)
|
||
("r-varselrf" ,r-varselrf)))
|
||
(home-page "https://bioconductor.org/packages/a4Classif/")
|
||
(synopsis "Automated Affymetrix array analysis classification package")
|
||
(description
|
||
"This is the classification package for the automated analysis of
|
||
Affymetrix arrays.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-a4preproc
|
||
(package
|
||
(name "r-a4preproc")
|
||
(version "1.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "a4Preproc" version))
|
||
(sha256
|
||
(base32
|
||
"13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
|
||
(properties `((upstream-name . "a4Preproc")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)))
|
||
(home-page "https://bioconductor.org/packages/a4Preproc/")
|
||
(synopsis "Automated Affymetrix array analysis preprocessing package")
|
||
(description
|
||
"This is a package for the automated analysis of Affymetrix arrays. It
|
||
is used for preprocessing the arrays.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-a4reporting
|
||
(package
|
||
(name "r-a4reporting")
|
||
(version "1.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "a4Reporting" version))
|
||
(sha256
|
||
(base32
|
||
"1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
|
||
(properties `((upstream-name . "a4Reporting")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annaffy" ,r-annaffy)
|
||
("r-xtable" ,r-xtable)))
|
||
(home-page "https://bioconductor.org/packages/a4Reporting/")
|
||
(synopsis "Automated Affymetrix array analysis reporting package")
|
||
(description
|
||
"This is a package for the automated analysis of Affymetrix arrays. It
|
||
provides reporting features.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-a4base
|
||
(package
|
||
(name "r-a4base")
|
||
(version "1.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "a4Base" version))
|
||
(sha256
|
||
(base32
|
||
"0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
|
||
(properties `((upstream-name . "a4Base")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-a4core" ,r-a4core)
|
||
("r-a4preproc" ,r-a4preproc)
|
||
("r-annaffy" ,r-annaffy)
|
||
("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-genefilter" ,r-genefilter)
|
||
("r-glmnet" ,r-glmnet)
|
||
("r-gplots" ,r-gplots)
|
||
("r-limma" ,r-limma)
|
||
("r-mpm" ,r-mpm)
|
||
("r-multtest" ,r-multtest)))
|
||
(home-page "https://bioconductor.org/packages/a4Base/")
|
||
(synopsis "Automated Affymetrix array analysis base package")
|
||
(description
|
||
"This package provides basic features for the automated analysis of
|
||
Affymetrix arrays.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-a4
|
||
(package
|
||
(name "r-a4")
|
||
(version "1.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "a4" version))
|
||
(sha256
|
||
(base32
|
||
"08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-a4base" ,r-a4base)
|
||
("r-a4classif" ,r-a4classif)
|
||
("r-a4core" ,r-a4core)
|
||
("r-a4preproc" ,r-a4preproc)
|
||
("r-a4reporting" ,r-a4reporting)))
|
||
(home-page "https://bioconductor.org/packages/a4/")
|
||
(synopsis "Automated Affymetrix array analysis umbrella package")
|
||
(description
|
||
"This package provides a software suite for the automated analysis of
|
||
Affymetrix arrays.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-abseqr
|
||
(package
|
||
(name "r-abseqr")
|
||
(version "1.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "abseqR" version))
|
||
(sha256
|
||
(base32
|
||
"0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
|
||
(properties `((upstream-name . "abseqR")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
`(("pandoc" ,ghc-pandoc)))
|
||
(propagated-inputs
|
||
`(("r-biocparallel" ,r-biocparallel)
|
||
("r-biocstyle" ,r-biocstyle)
|
||
("r-circlize" ,r-circlize)
|
||
("r-flexdashboard" ,r-flexdashboard)
|
||
("r-ggcorrplot" ,r-ggcorrplot)
|
||
("r-ggdendro" ,r-ggdendro)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-knitr" ,r-knitr)
|
||
("r-plotly" ,r-plotly)
|
||
("r-plyr" ,r-plyr)
|
||
("r-png" ,r-png)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-rmarkdown" ,r-rmarkdown)
|
||
("r-stringr" ,r-stringr)
|
||
("r-vegan" ,r-vegan)
|
||
("r-venndiagram" ,r-venndiagram)))
|
||
(home-page "https://github.com/malhamdoosh/abseqR")
|
||
(synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
|
||
(description
|
||
"AbSeq is a comprehensive bioinformatic pipeline for the analysis of
|
||
sequencing datasets generated from antibody libraries and abseqR is one of its
|
||
packages. AbseqR empowers the users of abseqPy with plotting and reporting
|
||
capabilities and allows them to generate interactive HTML reports for the
|
||
convenience of viewing and sharing with other researchers. Additionally,
|
||
abseqR extends abseqPy to compare multiple repertoire analyses and perform
|
||
further downstream analysis on its output.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-bacon
|
||
(package
|
||
(name "r-bacon")
|
||
(version "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "bacon" version))
|
||
(sha256
|
||
(base32
|
||
"1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocparallel" ,r-biocparallel)
|
||
("r-ellipse" ,r-ellipse)
|
||
("r-ggplot2" ,r-ggplot2)))
|
||
(home-page "https://bioconductor.org/packages/bacon/")
|
||
(synopsis "Controlling bias and inflation in association studies")
|
||
(description
|
||
"Bacon can be used to remove inflation and bias often observed in
|
||
epigenome- and transcriptome-wide association studies. To this end bacon
|
||
constructs an empirical null distribution using a Gibbs Sampling algorithm by
|
||
fitting a three-component normal mixture on z-scores.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rgadem
|
||
(package
|
||
(name "r-rgadem")
|
||
(version "2.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "rGADEM" version))
|
||
(sha256
|
||
(base32
|
||
"1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
|
||
(properties `((upstream-name . "rGADEM")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biostrings" ,r-biostrings)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-iranges" ,r-iranges)
|
||
("r-seqlogo" ,r-seqlogo)))
|
||
(home-page "https://bioconductor.org/packages/rGADEM/")
|
||
(synopsis "De novo sequence motif discovery")
|
||
(description
|
||
"rGADEM is an efficient de novo motif discovery tool for large-scale
|
||
genomic sequence data.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-motiv
|
||
(package
|
||
(name "r-motiv")
|
||
(version "1.40.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "MotIV" version))
|
||
(sha256
|
||
(base32
|
||
"088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
|
||
(properties `((upstream-name . "MotIV")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
`(("gsl" ,gsl)))
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-iranges" ,r-iranges)
|
||
("r-lattice" ,r-lattice)
|
||
("r-rgadem" ,r-rgadem)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/MotIV/")
|
||
(synopsis "Motif identification and validation")
|
||
(description
|
||
"This package is used for the identification and validation of sequence
|
||
motifs. It makes use of STAMP for comparing a set of motifs to a given
|
||
database (e.g. JASPAR). It can also be used to visualize motifs, motif
|
||
distributions, modules and filter motifs.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-motifstack
|
||
(package
|
||
(name "r-motifstack")
|
||
(version "1.28.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "motifStack" version))
|
||
(sha256
|
||
(base32
|
||
"0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
|
||
(properties `((upstream-name . "motifStack")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-ade4" ,r-ade4)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-grimport2" ,r-grimport2)
|
||
("r-htmlwidgets" ,r-htmlwidgets)
|
||
("r-motiv" ,r-motiv)
|
||
("r-scales" ,r-scales)
|
||
("r-xml" ,r-xml)))
|
||
(home-page "https://bioconductor.org/packages/motifStack/")
|
||
(synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
|
||
(description
|
||
"The motifStack package is designed for graphic representation of
|
||
multiple motifs with different similarity scores. It works with both DNA/RNA
|
||
sequence motifs and amino acid sequence motifs. In addition, it provides the
|
||
flexibility for users to customize the graphic parameters such as the font
|
||
type and symbol colors.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-genomicscores
|
||
(package
|
||
(name "r-genomicscores")
|
||
(version "1.8.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GenomicScores" version))
|
||
(sha256
|
||
(base32
|
||
"0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
|
||
(properties `((upstream-name . "GenomicScores")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationhub" ,r-annotationhub)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-xml" ,r-xml)))
|
||
(home-page "https://github.com/rcastelo/GenomicScores/")
|
||
(synopsis "Work with genome-wide position-specific scores")
|
||
(description
|
||
"This package provides infrastructure to store and access genome-wide
|
||
position-specific scores within R and Bioconductor.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-atacseqqc
|
||
(package
|
||
(name "r-atacseqqc")
|
||
(version "1.8.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ATACseqQC" version))
|
||
(sha256
|
||
(base32
|
||
"1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
|
||
(properties `((upstream-name . "ATACseqQC")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-chippeakanno" ,r-chippeakanno)
|
||
("r-edger" ,r-edger)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-genomicscores" ,r-genomicscores)
|
||
("r-iranges" ,r-iranges)
|
||
("r-kernsmooth" ,r-kernsmooth)
|
||
("r-limma" ,r-limma)
|
||
("r-motifstack" ,r-motifstack)
|
||
("r-preseqr" ,r-preseqr)
|
||
("r-randomforest" ,r-randomforest)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/ATACseqQC/")
|
||
(synopsis "ATAC-seq quality control")
|
||
(description
|
||
"ATAC-seq, an assay for Transposase-Accessible Chromatin using
|
||
sequencing, is a rapid and sensitive method for chromatin accessibility
|
||
analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
|
||
and DNAse-seq. The ATACseqQC package was developed to help users to quickly
|
||
assess whether their ATAC-seq experiment is successful. It includes
|
||
diagnostic plots of fragment size distribution, proportion of mitochondria
|
||
reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
|
||
footprints.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-gofuncr
|
||
(package
|
||
(name "r-gofuncr")
|
||
(version "1.4.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GOfuncR" version))
|
||
(sha256
|
||
(base32
|
||
"1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
|
||
(properties `((upstream-name . "GOfuncR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-gtools" ,r-gtools)
|
||
("r-iranges" ,r-iranges)
|
||
("r-mapplots" ,r-mapplots)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-vioplot" ,r-vioplot)))
|
||
(home-page "https://bioconductor.org/packages/GOfuncR/")
|
||
(synopsis "Gene ontology enrichment using FUNC")
|
||
(description
|
||
"GOfuncR performs a gene ontology enrichment analysis based on the
|
||
ontology enrichment software FUNC. GO-annotations are obtained from
|
||
OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
|
||
included in the package and updated regularly. GOfuncR provides the standard
|
||
candidate vs background enrichment analysis using the hypergeometric test, as
|
||
well as three additional tests:
|
||
|
||
@enumerate
|
||
@item the Wilcoxon rank-sum test that is used when genes are ranked,
|
||
@item a binomial test that is used when genes are associated with two counts,
|
||
and
|
||
@item a Chi-square or Fisher's exact test that is used in cases when genes are
|
||
associated with four counts.
|
||
@end enumerate
|
||
|
||
To correct for multiple testing and interdependency of the tests, family-wise
|
||
error rates are computed based on random permutations of the gene-associated
|
||
variables. GOfuncR also provides tools for exploring the ontology graph and
|
||
the annotations, and options to take gene-length or spatial clustering of
|
||
genes into account. It is also possible to provide custom gene coordinates,
|
||
annotations and ontologies.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-abaenrichment
|
||
(package
|
||
(name "r-abaenrichment")
|
||
(version "1.14.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ABAEnrichment" version))
|
||
(sha256
|
||
(base32
|
||
"1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
|
||
(properties `((upstream-name . "ABAEnrichment")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-abadata" ,r-abadata)
|
||
("r-data-table" ,r-data-table)
|
||
("r-gofuncr" ,r-gofuncr)
|
||
("r-gplots" ,r-gplots)
|
||
("r-gtools" ,r-gtools)
|
||
("r-rcpp" ,r-rcpp)))
|
||
(home-page "https://bioconductor.org/packages/ABAEnrichment/")
|
||
(synopsis "Gene expression enrichment in human brain regions")
|
||
(description
|
||
"The package ABAEnrichment is designed to test for enrichment of user
|
||
defined candidate genes in the set of expressed genes in different human brain
|
||
regions. The core function @code{aba_enrich} integrates the expression of the
|
||
candidate gene set (averaged across donors) and the structural information of
|
||
the brain using an ontology, both provided by the Allen Brain Atlas project.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-annotationfuncs
|
||
(package
|
||
(name "r-annotationfuncs")
|
||
(version "1.34.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "AnnotationFuncs" version))
|
||
(sha256
|
||
(base32
|
||
"12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
|
||
(properties
|
||
`((upstream-name . "AnnotationFuncs")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-dbi" ,r-dbi)))
|
||
(home-page "https://www.iysik.com/r/annotationfuncs")
|
||
(synopsis "Annotation translation functions")
|
||
(description
|
||
"This package provides functions for handling translating between
|
||
different identifieres using the Biocore Data Team data-packages (e.g.
|
||
@code{org.Bt.eg.db}).")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-annotationtools
|
||
(package
|
||
(name "r-annotationtools")
|
||
(version "1.58.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "annotationTools" version))
|
||
(sha256
|
||
(base32
|
||
"148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
|
||
(properties
|
||
`((upstream-name . "annotationTools")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs `(("r-biobase" ,r-biobase)))
|
||
(home-page "https://bioconductor.org/packages/annotationTools/")
|
||
(synopsis "Annotate microarrays and perform gene expression analyses")
|
||
(description
|
||
"This package provides functions to annotate microarrays, find orthologs,
|
||
and integrate heterogeneous gene expression profiles using annotation and
|
||
other molecular biology information available as flat file database (plain
|
||
text files).")
|
||
;; Any version of the GPL.
|
||
(license (list license:gpl2+))))
|
||
|
||
(define-public r-allelicimbalance
|
||
(package
|
||
(name "r-allelicimbalance")
|
||
(version "1.22.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "AllelicImbalance" version))
|
||
(sha256
|
||
(base32
|
||
"1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
|
||
(properties
|
||
`((upstream-name . "AllelicImbalance")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-gviz" ,r-gviz)
|
||
("r-iranges" ,r-iranges)
|
||
("r-lattice" ,r-lattice)
|
||
("r-latticeextra" ,r-latticeextra)
|
||
("r-nlme" ,r-nlme)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-seqinr" ,r-seqinr)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-variantannotation" ,r-variantannotation)))
|
||
(home-page "https://github.com/pappewaio/AllelicImbalance")
|
||
(synopsis "Investigate allele-specific expression")
|
||
(description
|
||
"This package provides a framework for allele-specific expression
|
||
investigation using RNA-seq data.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-aucell
|
||
(package
|
||
(name "r-aucell")
|
||
(version "1.6.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "AUCell" version))
|
||
(sha256
|
||
(base32
|
||
"1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
|
||
(properties `((upstream-name . "AUCell")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-data-table" ,r-data-table)
|
||
("r-gseabase" ,r-gseabase)
|
||
("r-mixtools" ,r-mixtools)
|
||
("r-r-utils" ,r-r-utils)
|
||
("r-shiny" ,r-shiny)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://bioconductor.org/packages/AUCell/")
|
||
(synopsis "Analysis of gene set activity in single-cell RNA-seq data")
|
||
(description
|
||
"AUCell allows to identify cells with active gene sets (e.g. signatures,
|
||
gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
|
||
Under the Curve} (AUC) to calculate whether a critical subset of the input
|
||
gene set is enriched within the expressed genes for each cell. The
|
||
distribution of AUC scores across all the cells allows exploring the relative
|
||
expression of the signature. Since the scoring method is ranking-based,
|
||
AUCell is independent of the gene expression units and the normalization
|
||
procedure. In addition, since the cells are evaluated individually, it can
|
||
easily be applied to bigger datasets, subsetting the expression matrix if
|
||
needed.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-ebimage
|
||
(package
|
||
(name "r-ebimage")
|
||
(version "4.26.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "EBImage" version))
|
||
(sha256
|
||
(base32
|
||
"0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
|
||
(properties `((upstream-name . "EBImage")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-abind" ,r-abind)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-fftwtools" ,r-fftwtools)
|
||
("r-htmltools" ,r-htmltools)
|
||
("r-htmlwidgets" ,r-htmlwidgets)
|
||
("r-jpeg" ,r-jpeg)
|
||
("r-locfit" ,r-locfit)
|
||
("r-png" ,r-png)
|
||
("r-rcurl" ,r-rcurl)
|
||
("r-tiff" ,r-tiff)))
|
||
(native-inputs
|
||
`(("r-knitr" ,r-knitr))) ; for vignettes
|
||
(home-page "https://github.com/aoles/EBImage")
|
||
(synopsis "Image processing and analysis toolbox for R")
|
||
(description
|
||
"EBImage provides general purpose functionality for image processing and
|
||
analysis. In the context of (high-throughput) microscopy-based cellular
|
||
assays, EBImage offers tools to segment cells and extract quantitative
|
||
cellular descriptors. This allows the automation of such tasks using the R
|
||
programming language and facilitates the use of other tools in the R
|
||
environment for signal processing, statistical modeling, machine learning and
|
||
visualization with image data.")
|
||
;; Any version of the LGPL.
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-yamss
|
||
(package
|
||
(name "r-yamss")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "yamss" version))
|
||
(sha256
|
||
(base32
|
||
"00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-data-table" ,r-data-table)
|
||
("r-ebimage" ,r-ebimage)
|
||
("r-iranges" ,r-iranges)
|
||
("r-limma" ,r-limma)
|
||
("r-matrix" ,r-matrix)
|
||
("r-mzr" ,r-mzr)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment"
|
||
,r-summarizedexperiment)))
|
||
(home-page "https://github.com/hansenlab/yamss")
|
||
(synopsis "Tools for high-throughput metabolomics")
|
||
(description
|
||
"This package provides tools to analyze and visualize high-throughput
|
||
metabolomics data acquired using chromatography-mass spectrometry. These tools
|
||
preprocess data in a way that enables reliable and powerful differential
|
||
analysis.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-gtrellis
|
||
(package
|
||
(name "r-gtrellis")
|
||
(version "1.16.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "gtrellis" version))
|
||
(sha256
|
||
(base32
|
||
"069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-circlize" ,r-circlize)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-getoptlong" ,r-getoptlong)
|
||
("r-iranges" ,r-iranges)))
|
||
(home-page "https://github.com/jokergoo/gtrellis")
|
||
(synopsis "Genome level Trellis layout")
|
||
(description
|
||
"Genome level Trellis graph visualizes genomic data conditioned by
|
||
genomic categories (e.g. chromosomes). For each genomic category, multiple
|
||
dimensional data which are represented as tracks describe different features
|
||
from different aspects. This package provides high flexibility to arrange
|
||
genomic categories and to add self-defined graphics in the plot.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-somaticsignatures
|
||
(package
|
||
(name "r-somaticsignatures")
|
||
(version "2.20.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "SomaticSignatures" version))
|
||
(sha256
|
||
(base32
|
||
"0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
|
||
(properties
|
||
`((upstream-name . "SomaticSignatures")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggbio" ,r-ggbio)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-iranges" ,r-iranges)
|
||
("r-nmf" ,r-nmf)
|
||
("r-pcamethods" ,r-pcamethods)
|
||
("r-proxy" ,r-proxy)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-variantannotation" ,r-variantannotation)))
|
||
(home-page "https://github.com/juliangehring/SomaticSignatures")
|
||
(synopsis "Somatic signatures")
|
||
(description
|
||
"This package identifies mutational signatures of @dfn{single nucleotide
|
||
variants} (SNVs). It provides a infrastructure related to the methodology
|
||
described in Nik-Zainal (2012, Cell), with flexibility in the matrix
|
||
decomposition algorithms.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-yapsa
|
||
(package
|
||
(name "r-yapsa")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "YAPSA" version))
|
||
(sha256
|
||
(base32
|
||
"0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
|
||
(properties `((upstream-name . "YAPSA")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-circlize" ,r-circlize)
|
||
("r-complexheatmap" ,r-complexheatmap)
|
||
("r-corrplot" ,r-corrplot)
|
||
("r-dendextend" ,r-dendextend)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-getoptlong" ,r-getoptlong)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-gtrellis" ,r-gtrellis)
|
||
("r-keggrest" ,r-keggrest)
|
||
("r-lsei" ,r-lsei)
|
||
("r-pmcmr" ,r-pmcmr)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-somaticsignatures" ,r-somaticsignatures)
|
||
("r-variantannotation" ,r-variantannotation)))
|
||
(home-page "https://bioconductor.org/packages/YAPSA/")
|
||
(synopsis "Yet another package for signature analysis")
|
||
(description
|
||
"This package provides functions and routines useful in the analysis of
|
||
somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
|
||
functions to perform a signature analysis with known signatures and a
|
||
signature analysis on @dfn{stratified mutational catalogue} (SMC) are
|
||
provided.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-gcrma
|
||
(package
|
||
(name "r-gcrma")
|
||
(version "2.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "gcrma" version))
|
||
(sha256
|
||
(base32
|
||
"1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-affy" ,r-affy)
|
||
("r-affyio" ,r-affyio)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocmanager" ,r-biocmanager)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-xvector" ,r-xvector)))
|
||
(home-page "https://bioconductor.org/packages/gcrma/")
|
||
(synopsis "Background adjustment using sequence information")
|
||
(description
|
||
"Gcrma adjusts for background intensities in Affymetrix array data which
|
||
include optical noise and @dfn{non-specific binding} (NSB). The main function
|
||
@code{gcrma} converts background adjusted probe intensities to expression
|
||
measures using the same normalization and summarization methods as a
|
||
@dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
|
||
to estimate probe affinity to NSB. The sequence information is summarized in
|
||
a more complex way than the simple GC content. Instead, the base types (A, T,
|
||
G or C) at each position along the probe determine the affinity of each probe.
|
||
The parameters of the position-specific base contributions to the probe
|
||
affinity is estimated in an NSB experiment in which only NSB but no
|
||
gene-specific bidning is expected.")
|
||
;; Any version of the LGPL
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-simpleaffy
|
||
(package
|
||
(name "r-simpleaffy")
|
||
(version "2.60.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "simpleaffy" version))
|
||
(sha256
|
||
(base32
|
||
"0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-affy" ,r-affy)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-gcrma" ,r-gcrma)
|
||
("r-genefilter" ,r-genefilter)))
|
||
(home-page "https://bioconductor.org/packages/simpleaffy/")
|
||
(synopsis "Very simple high level analysis of Affymetrix data")
|
||
(description
|
||
"This package provides high level functions for reading Affy @file{.CEL}
|
||
files, phenotypic data, and then computing simple things with it, such as
|
||
t-tests, fold changes and the like. It makes heavy use of the @code{affy}
|
||
library. It also has some basic scatter plot functions and mechanisms for
|
||
generating high resolution journal figures.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-yaqcaffy
|
||
(package
|
||
(name "r-yaqcaffy")
|
||
(version "1.44.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "yaqcaffy" version))
|
||
(sha256
|
||
(base32
|
||
"1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-simpleaffy" ,r-simpleaffy)))
|
||
(home-page "https://bioconductor.org/packages/yaqcaffy/")
|
||
(synopsis "Affymetrix quality control and reproducibility analysis")
|
||
(description
|
||
"This is a package that can be used for quality control of Affymetrix
|
||
GeneChip expression data and reproducibility analysis of human whole genome
|
||
chips with the MAQC reference datasets.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-quantro
|
||
(package
|
||
(name "r-quantro")
|
||
(version "1.18.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "quantro" version))
|
||
(sha256
|
||
(base32
|
||
"0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-doparallel" ,r-doparallel)
|
||
("r-foreach" ,r-foreach)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-iterators" ,r-iterators)
|
||
("r-minfi" ,r-minfi)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)))
|
||
(home-page "https://bioconductor.org/packages/quantro/")
|
||
(synopsis "Test for when to use quantile normalization")
|
||
(description
|
||
"This package provides a data-driven test for the assumptions of quantile
|
||
normalization using raw data such as objects that inherit eSets (e.g.
|
||
ExpressionSet, MethylSet). Group level information about each sample (such as
|
||
Tumor / Normal status) must also be provided because the test assesses if
|
||
there are global differences in the distributions between the user-defined
|
||
groups.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-yarn
|
||
(package
|
||
(name "r-yarn")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "yarn" version))
|
||
(sha256
|
||
(base32
|
||
"00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biomart" ,r-biomart)
|
||
("r-downloader" ,r-downloader)
|
||
("r-edger" ,r-edger)
|
||
("r-gplots" ,r-gplots)
|
||
("r-limma" ,r-limma)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-preprocesscore" ,r-preprocesscore)
|
||
("r-quantro" ,r-quantro)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||
("r-readr" ,r-readr)))
|
||
(home-page "https://bioconductor.org/packages/yarn/")
|
||
(synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
|
||
(description
|
||
"Expedite large RNA-Seq analyses using a combination of previously
|
||
developed tools. YARN is meant to make it easier for the user in performing
|
||
basic mis-annotation quality control, filtering, and condition-aware
|
||
normalization. YARN leverages many Bioconductor tools and statistical
|
||
techniques to account for the large heterogeneity and sparsity found in very
|
||
large RNA-seq experiments.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-roar
|
||
(package
|
||
(name "r-roar")
|
||
(version "1.20.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "roar" version))
|
||
(sha256
|
||
(base32
|
||
"11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://github.com/vodkatad/roar/")
|
||
(synopsis "Identify differential APA usage from RNA-seq alignments")
|
||
(description
|
||
"This package provides tools for identifying preferential usage of APA
|
||
sites, comparing two biological conditions, starting from known alternative
|
||
sites and alignments obtained from standard RNA-seq experiments.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-xbseq
|
||
(package
|
||
(name "r-xbseq")
|
||
(version "1.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "XBSeq" version))
|
||
(sha256
|
||
(base32
|
||
"12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
|
||
(properties `((upstream-name . "XBSeq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-deseq2" ,r-deseq2)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-locfit" ,r-locfit)
|
||
("r-magrittr" ,r-magrittr)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-pracma" ,r-pracma)
|
||
("r-roar" ,r-roar)))
|
||
(home-page "https://github.com/Liuy12/XBSeq")
|
||
(synopsis "Test for differential expression for RNA-seq data")
|
||
(description
|
||
"XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
|
||
expression} (DE), where a statistical model was established based on the
|
||
assumption that observed signals are the convolution of true expression
|
||
signals and sequencing noises. The mapped reads in non-exonic regions are
|
||
considered as sequencing noises, which follows a Poisson distribution. Given
|
||
measurable observed signal and background noise from RNA-seq data, true
|
||
expression signals, assuming governed by the negative binomial distribution,
|
||
can be delineated and thus the accurate detection of differential expressed
|
||
genes.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-massspecwavelet
|
||
(package
|
||
(name "r-massspecwavelet")
|
||
(version "1.50.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "MassSpecWavelet" version))
|
||
(sha256
|
||
(base32
|
||
"1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
|
||
(properties
|
||
`((upstream-name . "MassSpecWavelet")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-waveslim" ,r-waveslim)))
|
||
(home-page "https://bioconductor.org/packages/MassSpecWavelet/")
|
||
(synopsis "Mass spectrum processing by wavelet-based algorithms")
|
||
(description
|
||
"The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
|
||
data mainly through the use of wavelet transforms. It supports peak detection
|
||
based on @dfn{Continuous Wavelet Transform} (CWT).")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-xcms
|
||
(package
|
||
(name "r-xcms")
|
||
(version "3.6.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "xcms" version))
|
||
(sha256
|
||
(base32
|
||
"06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-lattice" ,r-lattice)
|
||
("r-massspecwavelet" ,r-massspecwavelet)
|
||
("r-msnbase" ,r-msnbase)
|
||
("r-multtest" ,r-multtest)
|
||
("r-mzr" ,r-mzr)
|
||
("r-plyr" ,r-plyr)
|
||
("r-protgenerics" ,r-protgenerics)
|
||
("r-rann" ,r-rann)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||
("r-robustbase" ,r-robustbase)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/xcms/")
|
||
(synopsis "LC/MS and GC/MS mass spectrometry data analysis")
|
||
(description
|
||
"This package provides a framework for processing and visualization of
|
||
chromatographically separated and single-spectra mass spectral data. It
|
||
imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
|
||
data for high-throughput, untargeted analyte profiling.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-wrench
|
||
(package
|
||
(name "r-wrench")
|
||
(version "1.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Wrench" version))
|
||
(sha256
|
||
(base32
|
||
"1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
|
||
(properties `((upstream-name . "Wrench")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-limma" ,r-limma)
|
||
("r-locfit" ,r-locfit)
|
||
("r-matrixstats" ,r-matrixstats)))
|
||
(home-page "https://github.com/HCBravoLab/Wrench")
|
||
(synopsis "Wrench normalization for sparse count data")
|
||
(description
|
||
"Wrench is a package for normalization sparse genomic count data, like
|
||
that arising from 16s metagenomic surveys.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-wiggleplotr
|
||
(package
|
||
(name "r-wiggleplotr")
|
||
(version "1.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "wiggleplotr" version))
|
||
(sha256
|
||
(base32
|
||
"0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-assertthat" ,r-assertthat)
|
||
("r-cowplot" ,r-cowplot)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-iranges" ,r-iranges)
|
||
("r-purrr" ,r-purrr)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/wiggleplotr/")
|
||
(synopsis "Make read coverage plots from BigWig files")
|
||
(description
|
||
"This package provides tools to visualize read coverage from sequencing
|
||
experiments together with genomic annotations (genes, transcripts, peaks).
|
||
Introns of long transcripts can be rescaled to a fixed length for better
|
||
visualization of exonic read coverage.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public r-widgettools
|
||
(package
|
||
(name "r-widgettools")
|
||
(version "1.62.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "widgetTools" version))
|
||
(sha256
|
||
(base32
|
||
"021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
|
||
(properties `((upstream-name . "widgetTools")))
|
||
(build-system r-build-system)
|
||
(home-page "https://bioconductor.org/packages/widgetTools/")
|
||
(synopsis "Tools for creating interactive tcltk widgets")
|
||
(description
|
||
"This package contains tools to support the construction of tcltk
|
||
widgets in R.")
|
||
;; Any version of the LGPL.
|
||
(license license:lgpl3+)))
|
||
|
||
(define-public r-webbioc
|
||
(package
|
||
(name "r-webbioc")
|
||
(version "1.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "webbioc" version))
|
||
(sha256
|
||
(base32
|
||
"0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
`(("netpbm" ,netpbm)
|
||
("perl" ,perl)))
|
||
(propagated-inputs
|
||
`(("r-affy" ,r-affy)
|
||
("r-annaffy" ,r-annaffy)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocmanager" ,r-biocmanager)
|
||
("r-gcrma" ,r-gcrma)
|
||
("r-multtest" ,r-multtest)
|
||
("r-qvalue" ,r-qvalue)
|
||
("r-vsn" ,r-vsn)))
|
||
(home-page "https://www.bioconductor.org/")
|
||
(synopsis "Bioconductor web interface")
|
||
(description
|
||
"This package provides an integrated web interface for doing microarray
|
||
analysis using several of the Bioconductor packages. It is intended to be
|
||
deployed as a centralized bioinformatics resource for use by many users.
|
||
Currently only Affymetrix oligonucleotide analysis is supported.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-zfpkm
|
||
(package
|
||
(name "r-zfpkm")
|
||
(version "1.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "zFPKM" version))
|
||
(sha256
|
||
(base32
|
||
"14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
|
||
(properties `((upstream-name . "zFPKM")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-checkmate" ,r-checkmate)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-tidyr" ,r-tidyr)))
|
||
(home-page "https://github.com/ronammar/zFPKM/")
|
||
(synopsis "Functions to facilitate zFPKM transformations")
|
||
(description
|
||
"This is a package to perform the zFPKM transform on RNA-seq FPKM data.
|
||
This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
|
||
24215113).")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-rbowtie2
|
||
(package
|
||
(name "r-rbowtie2")
|
||
(version "1.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Rbowtie2" version))
|
||
(sha256
|
||
(base32
|
||
"1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
|
||
(properties `((upstream-name . "Rbowtie2")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
`(("zlib" ,zlib)))
|
||
(home-page "https://bioconductor.org/packages/Rbowtie2/")
|
||
(synopsis "R wrapper for Bowtie2 and AdapterRemoval")
|
||
(description
|
||
"This package provides an R wrapper of the popular @code{bowtie2}
|
||
sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
|
||
rapid adapter trimming, identification, and read merging.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-progeny
|
||
(package
|
||
(name "r-progeny")
|
||
(version "1.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "progeny" version))
|
||
(sha256
|
||
(base32
|
||
"03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs `(("r-biobase" ,r-biobase)))
|
||
(home-page "https://github.com/saezlab/progeny")
|
||
(synopsis "Pathway responsive gene activity inference")
|
||
(description
|
||
"This package provides a function to infer pathway activity from gene
|
||
expression. It contains the linear model inferred in the publication
|
||
\"Perturbation-response genes reveal signaling footprints in cancer gene
|
||
expression\".")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public r-arrmnormalization
|
||
(package
|
||
(name "r-arrmnormalization")
|
||
(version "1.24.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ARRmNormalization" version))
|
||
(sha256
|
||
(base32
|
||
"05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
|
||
(properties
|
||
`((upstream-name . "ARRmNormalization")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
|
||
(home-page "https://bioconductor.org/packages/ARRmNormalization/")
|
||
(synopsis "Adaptive robust regression normalization for methylation data")
|
||
(description
|
||
"This is a package to perform the @dfn{Adaptive Robust Regression
|
||
method} (ARRm) for the normalization of methylation data from the Illumina
|
||
Infinium HumanMethylation 450k assay.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-biocfilecache
|
||
(package
|
||
(name "r-biocfilecache")
|
||
(version "1.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "BiocFileCache" version))
|
||
(sha256
|
||
(base32
|
||
"1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
|
||
(properties `((upstream-name . "BiocFileCache")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-curl" ,r-curl)
|
||
("r-dbi" ,r-dbi)
|
||
("r-dbplyr" ,r-dbplyr)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-httr" ,r-httr)
|
||
("r-rappdirs" ,r-rappdirs)
|
||
("r-rsqlite" ,r-rsqlite)))
|
||
(home-page "https://bioconductor.org/packages/BiocFileCache/")
|
||
(synopsis "Manage files across sessions")
|
||
(description
|
||
"This package creates a persistent on-disk cache of files that the user
|
||
can add, update, and retrieve. It is useful for managing resources (such as
|
||
custom Txdb objects) that are costly or difficult to create, web resources,
|
||
and data files used across sessions.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-iclusterplus
|
||
(package
|
||
(name "r-iclusterplus")
|
||
(version "1.20.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "iClusterPlus" version))
|
||
(sha256
|
||
(base32
|
||
"14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
|
||
(properties `((upstream-name . "iClusterPlus")))
|
||
(build-system r-build-system)
|
||
(native-inputs `(("gfortran" ,gfortran)))
|
||
(home-page "https://bioconductor.org/packages/iClusterPlus/")
|
||
(synopsis "Integrative clustering of multi-type genomic data")
|
||
(description
|
||
"iClusterPlus is developed for integrative clustering analysis of
|
||
multi-type genomic data and is an enhanced version of iCluster proposed and
|
||
developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
|
||
from the experiments where biological samples (e.g. tumor samples) are
|
||
analyzed by multiple techniques, for instance, @dfn{array comparative genomic
|
||
hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
|
||
on. In the iClusterPlus model, binary observations such as somatic mutation
|
||
are modeled as Binomial processes; categorical observations such as copy
|
||
number states are realizations of Multinomial random variables; counts are
|
||
modeled as Poisson random processes; and continuous measures are modeled by
|
||
Gaussian distributions.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rbowtie
|
||
(package
|
||
(name "r-rbowtie")
|
||
(version "1.24.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Rbowtie" version))
|
||
(sha256
|
||
(base32
|
||
"1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
|
||
(properties `((upstream-name . "Rbowtie")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
`(("zlib" ,zlib)))
|
||
(home-page "https://bioconductor.org/packages/Rbowtie/")
|
||
(synopsis "R bowtie wrapper")
|
||
(description
|
||
"This package provides an R wrapper around the popular bowtie short read
|
||
aligner and around SpliceMap, a de novo splice junction discovery and
|
||
alignment tool.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-sgseq
|
||
(package
|
||
(name "r-sgseq")
|
||
(version "1.18.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "SGSeq" version))
|
||
(sha256
|
||
(base32
|
||
"09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
|
||
(properties `((upstream-name . "SGSeq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-igraph" ,r-igraph)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-runit" ,r-runit)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://bioconductor.org/packages/SGSeq/")
|
||
(synopsis "Splice event prediction and quantification from RNA-seq data")
|
||
(description
|
||
"SGSeq is a package for analyzing splice events from RNA-seq data. Input
|
||
data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
|
||
represented as a splice graph, which can be obtained from existing annotation
|
||
or predicted from the mapped sequence reads. Splice events are identified
|
||
from the graph and are quantified locally using structurally compatible reads
|
||
at the start or end of each splice variant. The software includes functions
|
||
for splice event prediction, quantification, visualization and
|
||
interpretation.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-rhisat2
|
||
(package
|
||
(name "r-rhisat2")
|
||
(version "1.0.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Rhisat2" version))
|
||
(sha256
|
||
(base32
|
||
"02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
|
||
(properties `((upstream-name . "Rhisat2")))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
`(("which" ,which)))
|
||
(propagated-inputs
|
||
`(("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-sgseq" ,r-sgseq)))
|
||
(home-page "https://github.com/fmicompbio/Rhisat2")
|
||
(synopsis "R Wrapper for HISAT2 sequence aligner")
|
||
(description
|
||
"This package provides an R interface to the HISAT2 spliced short-read
|
||
aligner by Kim et al. (2015). The package contains wrapper functions to
|
||
create a genome index and to perform the read alignment to the generated
|
||
index.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-quasr
|
||
(package
|
||
(name "r-quasr")
|
||
(version "1.24.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "QuasR" version))
|
||
(sha256
|
||
(base32
|
||
"1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
|
||
(properties `((upstream-name . "QuasR")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
`(("zlib" ,zlib)))
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocmanager" ,r-biocmanager)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicfiles" ,r-genomicfiles)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rbowtie" ,r-rbowtie)
|
||
("r-rhisat2" ,r-rhisat2)
|
||
("r-rhtslib" ,r-rhtslib)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-shortread" ,r-shortread)))
|
||
(home-page "https://bioconductor.org/packages/QuasR/")
|
||
(synopsis "Quantify and annotate short reads in R")
|
||
(description
|
||
"This package provides a framework for the quantification and analysis of
|
||
short genomic reads. It covers a complete workflow starting from raw sequence
|
||
reads, over creation of alignments and quality control plots, to the
|
||
quantification of genomic regions of interest.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-rqc
|
||
(package
|
||
(name "r-rqc")
|
||
(version "1.18.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Rqc" version))
|
||
(sha256
|
||
(base32
|
||
"09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
|
||
(properties `((upstream-name . "Rqc")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-biocstyle" ,r-biocstyle)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-biovizbase" ,r-biovizbase)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicfiles" ,r-genomicfiles)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-iranges" ,r-iranges)
|
||
("r-knitr" ,r-knitr)
|
||
("r-markdown" ,r-markdown)
|
||
("r-plyr" ,r-plyr)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-shiny" ,r-shiny)
|
||
("r-shortread" ,r-shortread)))
|
||
(home-page "https://github.com/labbcb/Rqc")
|
||
(synopsis "Quality control tool for high-throughput sequencing data")
|
||
(description
|
||
"Rqc is an optimized tool designed for quality control and assessment of
|
||
high-throughput sequencing data. It performs parallel processing of entire
|
||
files and produces a report which contains a set of high-resolution
|
||
graphics.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-birewire
|
||
(package
|
||
(name "r-birewire")
|
||
(version "3.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "BiRewire" version))
|
||
(sha256
|
||
(base32
|
||
"1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
|
||
(properties `((upstream-name . "BiRewire")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-igraph" ,r-igraph)
|
||
("r-matrix" ,r-matrix)
|
||
("r-slam" ,r-slam)
|
||
("r-tsne" ,r-tsne)))
|
||
(home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
|
||
(synopsis "Tools for randomization of bipartite graphs")
|
||
(description
|
||
"This package provides functions for bipartite network rewiring through N
|
||
consecutive switching steps and for the computation of the minimal number of
|
||
switching steps to be performed in order to maximise the dissimilarity with
|
||
respect to the original network. It includes functions for the analysis of
|
||
the introduced randomness across the switching steps and several other
|
||
routines to analyse the resulting networks and their natural projections.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-birta
|
||
(package
|
||
(name "r-birta")
|
||
(version "1.28.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "birta" version))
|
||
(sha256
|
||
(base32
|
||
"12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-limma" ,r-limma)
|
||
("r-mass" ,r-mass)))
|
||
(home-page "https://bioconductor.org/packages/birta")
|
||
(synopsis "Bayesian inference of regulation of transcriptional activity")
|
||
(description
|
||
"Expression levels of mRNA molecules are regulated by different
|
||
processes, comprising inhibition or activation by transcription factors and
|
||
post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
|
||
Inference of Regulation of Transcriptional Activity) uses the regulatory
|
||
networks of transcription factors and miRNAs together with mRNA and miRNA
|
||
expression data to predict switches in regulatory activity between two
|
||
conditions. A Bayesian network is used to model the regulatory structure and
|
||
Markov-Chain-Monte-Carlo is applied to sample the activity states.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-ropls
|
||
(package
|
||
(name "r-ropls")
|
||
(version "1.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ropls" version))
|
||
(sha256
|
||
(base32
|
||
"099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs `(("r-biobase" ,r-biobase)))
|
||
(native-inputs
|
||
`(("r-knitr" ,r-knitr))) ; for vignettes
|
||
(home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
|
||
(synopsis "Multivariate analysis and feature selection of omics data")
|
||
(description
|
||
"Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
|
||
and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
|
||
regression, classification, and feature selection of omics data where the
|
||
number of variables exceeds the number of samples and with multicollinearity
|
||
among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
|
||
separately model the variation correlated (predictive) to the factor of
|
||
interest and the uncorrelated (orthogonal) variation. While performing
|
||
similarly to PLS, OPLS facilitates interpretation.
|
||
|
||
This package provides imlementations of PCA, PLS, and OPLS for multivariate
|
||
analysis and feature selection of omics data. In addition to scores, loadings
|
||
and weights plots, the package provides metrics and graphics to determine the
|
||
optimal number of components (e.g. with the R2 and Q2 coefficients), check the
|
||
validity of the model by permutation testing, detect outliers, and perform
|
||
feature selection (e.g. with Variable Importance in Projection or regression
|
||
coefficients).")
|
||
(license license:cecill)))
|
||
|
||
(define-public r-biosigner
|
||
(package
|
||
(name "r-biosigner")
|
||
(version "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "biosigner" version))
|
||
(sha256
|
||
(base32
|
||
"1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-e1071" ,r-e1071)
|
||
("r-randomforest" ,r-randomforest)
|
||
("r-ropls" ,r-ropls)))
|
||
(native-inputs
|
||
`(("r-knitr" ,r-knitr)
|
||
("r-rmarkdown" ,r-rmarkdown)
|
||
("pandoc" ,ghc-pandoc)
|
||
("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
|
||
(home-page "https://bioconductor.org/packages/biosigner/")
|
||
(synopsis "Signature discovery from omics data")
|
||
(description
|
||
"Feature selection is critical in omics data analysis to extract
|
||
restricted and meaningful molecular signatures from complex and high-dimension
|
||
data, and to build robust classifiers. This package implements a method to
|
||
assess the relevance of the variables for the prediction performances of the
|
||
classifier. The approach can be run in parallel with the PLS-DA, Random
|
||
Forest, and SVM binary classifiers. The signatures and the corresponding
|
||
'restricted' models are returned, enabling future predictions on new
|
||
datasets.")
|
||
(license license:cecill)))
|
||
|
||
(define-public r-annotatr
|
||
(package
|
||
(name "r-annotatr")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "annotatr" version))
|
||
(sha256
|
||
(base32
|
||
"1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-annotationhub" ,r-annotationhub)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-iranges" ,r-iranges)
|
||
("r-readr" ,r-readr)
|
||
("r-regioner" ,r-regioner)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/annotatr/")
|
||
(synopsis "Annotation of genomic regions to genomic annotations")
|
||
(description
|
||
"Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
|
||
differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
|
||
to investigate the intersecting genomic annotations. Such annotations include
|
||
those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
|
||
CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
|
||
enhancers. The annotatr package provides an easy way to summarize and
|
||
visualize the intersection of genomic sites/regions with genomic
|
||
annotations.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-rsubread
|
||
(package
|
||
(name "r-rsubread")
|
||
(version "1.34.7")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Rsubread" version))
|
||
(sha256
|
||
(base32
|
||
"0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
|
||
(properties `((upstream-name . "Rsubread")))
|
||
(build-system r-build-system)
|
||
(inputs `(("zlib" ,zlib)))
|
||
(home-page "https://bioconductor.org/packages/Rsubread/")
|
||
(synopsis "Subread sequence alignment and counting for R")
|
||
(description
|
||
"This package provides tools for alignment, quantification and analysis
|
||
of second and third generation sequencing data. It includes functionality for
|
||
read mapping, read counting, SNP calling, structural variant detection and
|
||
gene fusion discovery. It can be applied to all major sequencing techologies
|
||
and to both short and long sequence reads.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-flowutils
|
||
(package
|
||
(name "r-flowutils")
|
||
(version "1.48.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "flowUtils" version))
|
||
(sha256
|
||
(base32
|
||
"1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
|
||
(properties `((upstream-name . "flowUtils")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-corpcor" ,r-corpcor)
|
||
("r-flowcore" ,r-flowcore)
|
||
("r-graph" ,r-graph)
|
||
("r-runit" ,r-runit)
|
||
("r-xml" ,r-xml)))
|
||
(home-page "https://github.com/jspidlen/flowUtils")
|
||
(synopsis "Utilities for flow cytometry")
|
||
(description
|
||
"This package provides utilities for flow cytometry data.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-consensusclusterplus
|
||
(package
|
||
(name "r-consensusclusterplus")
|
||
(version "1.48.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ConsensusClusterPlus" version))
|
||
(sha256
|
||
(base32
|
||
"1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
|
||
(properties
|
||
`((upstream-name . "ConsensusClusterPlus")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-all" ,r-all)
|
||
("r-biobase" ,r-biobase)
|
||
("r-cluster" ,r-cluster)))
|
||
(home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
|
||
(synopsis "Clustering algorithm")
|
||
(description
|
||
"This package provides an implementation of an algorithm for determining
|
||
cluster count and membership by stability evidence in unsupervised analysis.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-flowcore
|
||
(package
|
||
(name "r-flowcore")
|
||
(version "1.50.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "flowCore" version))
|
||
(sha256
|
||
(base32
|
||
"0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
|
||
(properties `((upstream-name . "flowCore")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-bh" ,r-bh)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-corpcor" ,r-corpcor)
|
||
("r-graph" ,r-graph)
|
||
("r-mass" ,r-mass)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rrcov" ,r-rrcov)))
|
||
(home-page "https://bioconductor.org/packages/flowCore")
|
||
(synopsis "Basic structures for flow cytometry data")
|
||
(description
|
||
"This package provides S4 data structures and basic functions to deal
|
||
with flow cytometry data.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-flowmeans
|
||
(package
|
||
(name "r-flowmeans")
|
||
(version "1.44.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "flowMeans" version))
|
||
(sha256
|
||
(base32
|
||
"0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
|
||
(properties `((upstream-name . "flowMeans")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-feature" ,r-feature)
|
||
("r-flowcore" ,r-flowcore)
|
||
("r-rrcov" ,r-rrcov)))
|
||
(home-page "https://bioconductor.org/packages/flowMeans")
|
||
(synopsis "Non-parametric flow cytometry data gating")
|
||
(description
|
||
"This package provides tools to identify cell populations in Flow
|
||
Cytometry data using non-parametric clustering and segmented-regression-based
|
||
change point detection.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-flowsom
|
||
(package
|
||
(name "r-flowsom")
|
||
(version "1.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "FlowSOM" version))
|
||
(sha256
|
||
(base32
|
||
"03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
|
||
(properties `((upstream-name . "FlowSOM")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-consensusclusterplus" ,r-consensusclusterplus)
|
||
("r-flowcore" ,r-flowcore)
|
||
("r-flowutils" ,r-flowutils)
|
||
("r-igraph" ,r-igraph)
|
||
("r-tsne" ,r-tsne)
|
||
("r-xml" ,r-xml)))
|
||
(home-page "https://bioconductor.org/packages/FlowSOM/")
|
||
(synopsis "Visualize and interpret cytometry data")
|
||
(description
|
||
"FlowSOM offers visualization options for cytometry data, by using
|
||
self-organizing map clustering and minimal spanning trees.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-mixomics
|
||
(package
|
||
(name "r-mixomics")
|
||
(version "6.8.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "mixOmics" version))
|
||
(sha256
|
||
(base32
|
||
"0lw4c9lxcm83xrvl4y120i1z710qjbdqginhrw738azpr1f82hcg"))))
|
||
(properties `((upstream-name . "mixOmics")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-corpcor" ,r-corpcor)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-ellipse" ,r-ellipse)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-igraph" ,r-igraph)
|
||
("r-lattice" ,r-lattice)
|
||
("r-mass" ,r-mass)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-rarpack" ,r-rarpack)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-tidyr" ,r-tidyr)))
|
||
(home-page "http://www.mixOmics.org")
|
||
(synopsis "Multivariate methods for exploration of biological datasets")
|
||
(description
|
||
"mixOmics offers a wide range of multivariate methods for the exploration
|
||
and integration of biological datasets with a particular focus on variable
|
||
selection. The package proposes several sparse multivariate models we have
|
||
developed to identify the key variables that are highly correlated, and/or
|
||
explain the biological outcome of interest. The data that can be analysed
|
||
with mixOmics may come from high throughput sequencing technologies, such as
|
||
omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
|
||
also beyond the realm of omics (e.g. spectral imaging). The methods
|
||
implemented in mixOmics can also handle missing values without having to
|
||
delete entire rows with missing data.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-depecher
|
||
(package
|
||
(name "r-depecher")
|
||
(version "1.0.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DepecheR" version))
|
||
(sha256
|
||
(base32
|
||
"0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
|
||
(properties `((upstream-name . "DepecheR")))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'fix-syntax-error
|
||
(lambda _
|
||
(substitute* "src/Makevars"
|
||
((" & ") " && "))
|
||
#t)))))
|
||
(propagated-inputs
|
||
`(("r-beanplot" ,r-beanplot)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-dosnow" ,r-dosnow)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-foreach" ,r-foreach)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gplots" ,r-gplots)
|
||
("r-mass" ,r-mass)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-mixomics" ,r-mixomics)
|
||
("r-moments" ,r-moments)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rcppeigen" ,r-rcppeigen)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-viridis" ,r-viridis)))
|
||
(home-page "https://bioconductor.org/packages/DepecheR/")
|
||
(synopsis "Identify traits of clusters in high-dimensional entities")
|
||
(description
|
||
"The purpose of this package is to identify traits in a dataset that can
|
||
separate groups. This is done on two levels. First, clustering is performed,
|
||
using an implementation of sparse K-means. Secondly, the generated clusters
|
||
are used to predict outcomes of groups of individuals based on their
|
||
distribution of observations in the different clusters. As certain clusters
|
||
with separating information will be identified, and these clusters are defined
|
||
by a sparse number of variables, this method can reduce the complexity of
|
||
data, to only emphasize the data that actually matters.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-rcistarget
|
||
(package
|
||
(name "r-rcistarget")
|
||
(version "1.4.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RcisTarget" version))
|
||
(sha256
|
||
(base32
|
||
"133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
|
||
(properties `((upstream-name . "RcisTarget")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-aucell" ,r-aucell)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-data-table" ,r-data-table)
|
||
("r-feather" ,r-feather)
|
||
("r-gseabase" ,r-gseabase)
|
||
("r-r-utils" ,r-r-utils)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://aertslab.org/#scenic")
|
||
(synopsis "Identify transcription factor binding motifs enriched on a gene list")
|
||
(description
|
||
"RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
|
||
over-represented on a gene list. In a first step, RcisTarget selects DNA
|
||
motifs that are significantly over-represented in the surroundings of the
|
||
@dfn{transcription start site} (TSS) of the genes in the gene-set. This is
|
||
achieved by using a database that contains genome-wide cross-species rankings
|
||
for each motif. The motifs that are then annotated to TFs and those that have
|
||
a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
|
||
each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
|
||
genes in the gene-set that are ranked above the leading edge).")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-cicero
|
||
(package
|
||
(name "r-cicero")
|
||
(version "1.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "cicero" version))
|
||
(sha256
|
||
(base32
|
||
"0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-assertthat" ,r-assertthat)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-data-table" ,r-data-table)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-fnn" ,r-fnn)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-glasso" ,r-glasso)
|
||
("r-gviz" ,r-gviz)
|
||
("r-igraph" ,r-igraph)
|
||
("r-iranges" ,r-iranges)
|
||
("r-matrix" ,r-matrix)
|
||
("r-monocle" ,r-monocle)
|
||
("r-plyr" ,r-plyr)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-stringr" ,r-stringr)
|
||
("r-tibble" ,r-tibble)
|
||
("r-vgam" ,r-vgam)))
|
||
(home-page "https://bioconductor.org/packages/cicero/")
|
||
(synopsis "Predict cis-co-accessibility from single-cell data")
|
||
(description
|
||
"Cicero computes putative cis-regulatory maps from single-cell chromatin
|
||
accessibility data. It also extends the monocle package for use in chromatin
|
||
accessibility data.")
|
||
(license license:expat)))
|
||
|
||
;; This is the latest commit on the "monocle3" branch.
|
||
(define-public r-cicero-monocle3
|
||
(let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
|
||
(revision "1"))
|
||
(package (inherit r-cicero)
|
||
(name "r-cicero-monocle3")
|
||
(version (git-version "1.3.2" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/cole-trapnell-lab/cicero-release.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
|
||
(propagated-inputs
|
||
`(("r-monocle3" ,r-monocle3)
|
||
,@(alist-delete "r-monocle"
|
||
(package-propagated-inputs r-cicero)))))))
|
||
|
||
(define-public r-cistopic
|
||
(let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
|
||
(revision "0"))
|
||
(package
|
||
(name "r-cistopic")
|
||
(version (git-version "0.2.1" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/aertslab/cisTopic.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-aucell" ,r-aucell)
|
||
("r-data-table" ,r-data-table)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-dosnow" ,r-dosnow)
|
||
("r-dt" ,r-dt)
|
||
("r-feather" ,r-feather)
|
||
("r-fitdistrplus" ,r-fitdistrplus)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-lda" ,r-lda)
|
||
("r-matrix" ,r-matrix)
|
||
("r-plyr" ,r-plyr)
|
||
("r-rcistarget" ,r-rcistarget)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://github.com/aertslab/cisTopic")
|
||
(synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
|
||
(description
|
||
"The sparse nature of single cell epigenomics data can be overruled using
|
||
probabilistic modelling methods such as @dfn{Latent Dirichlet
|
||
Allocation} (LDA). This package allows the probabilistic modelling of
|
||
cis-regulatory topics (cisTopics) from single cell epigenomics data, and
|
||
includes functionalities to identify cell states based on the contribution of
|
||
cisTopics and explore the nature and regulatory proteins driving them.")
|
||
(license license:gpl3))))
|
||
|
||
(define-public r-genie3
|
||
(package
|
||
(name "r-genie3")
|
||
(version "1.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GENIE3" version))
|
||
(sha256
|
||
(base32
|
||
"0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
|
||
(properties `((upstream-name . "GENIE3")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs `(("r-reshape2" ,r-reshape2)))
|
||
(home-page "https://bioconductor.org/packages/GENIE3")
|
||
(synopsis "Gene network inference with ensemble of trees")
|
||
(description
|
||
"This package implements the GENIE3 algorithm for inferring gene
|
||
regulatory networks from expression data.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-roc
|
||
(package
|
||
(name "r-roc")
|
||
(version "1.60.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ROC" version))
|
||
(sha256
|
||
(base32
|
||
"1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
|
||
(properties `((upstream-name . "ROC")))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.bioconductor.org/packages/ROC/")
|
||
(synopsis "Utilities for ROC curves")
|
||
(description
|
||
"This package provides utilities for @dfn{Receiver Operating
|
||
Characteristic} (ROC) curves, with a focus on micro arrays.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
|
||
(package
|
||
(name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
|
||
(version "0.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri
|
||
"IlluminaHumanMethylation450kanno.ilmn12.hg19"
|
||
version 'annotation))
|
||
(sha256
|
||
(base32
|
||
"059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
|
||
(properties
|
||
`((upstream-name
|
||
. "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs `(("r-minfi" ,r-minfi)))
|
||
(home-page
|
||
"https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
|
||
(synopsis "Annotation for Illumina's 450k methylation arrays")
|
||
(description
|
||
"This package provides manifests and annotation for Illumina's 450k array
|
||
data.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-watermelon
|
||
(package
|
||
(name "r-watermelon")
|
||
(version "1.28.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "wateRmelon" version))
|
||
(sha256
|
||
(base32
|
||
"0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
|
||
(properties `((upstream-name . "wateRmelon")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-illuminahumanmethylation450kanno-ilmn12-hg19"
|
||
,r-illuminahumanmethylation450kanno-ilmn12-hg19)
|
||
("r-illuminaio" ,r-illuminaio)
|
||
("r-limma" ,r-limma)
|
||
("r-lumi" ,r-lumi)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-methylumi" ,r-methylumi)
|
||
("r-roc" ,r-roc)))
|
||
(home-page "https://bioconductor.org/packages/wateRmelon/")
|
||
(synopsis "Illumina 450 methylation array normalization and metrics")
|
||
(description
|
||
"The standard index of DNA methylation (beta) is computed from methylated
|
||
and unmethylated signal intensities. Betas calculated from raw signal
|
||
intensities perform well, but using 11 methylomic datasets we demonstrate that
|
||
quantile normalization methods produce marked improvement. The commonly used
|
||
procedure of normalizing betas is inferior to the separate normalization of M
|
||
and U, and it is also advantageous to normalize Type I and Type II assays
|
||
separately. This package provides 15 flavours of betas and three performance
|
||
metrics, with methods for objects produced by the @code{methylumi} and
|
||
@code{minfi} packages.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-gdsfmt
|
||
(package
|
||
(name "r-gdsfmt")
|
||
(version "1.20.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "gdsfmt" version))
|
||
(sha256
|
||
(base32
|
||
"0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
|
||
(modules '((guix build utils)))
|
||
;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
|
||
;; them and link with system libraries instead.
|
||
(snippet
|
||
'(begin
|
||
(for-each delete-file-recursively
|
||
'("src/LZ4"
|
||
"src/XZ"
|
||
"src/ZLIB"))
|
||
(substitute* "src/Makevars"
|
||
(("all: \\$\\(SHLIB\\)") "all:")
|
||
(("\\$\\(SHLIB\\): liblzma.a") "")
|
||
(("(ZLIB|LZ4)/.*") "")
|
||
(("CoreArray/dVLIntGDS.cpp.*")
|
||
"CoreArray/dVLIntGDS.cpp")
|
||
(("CoreArray/dVLIntGDS.o.*")
|
||
"CoreArray/dVLIntGDS.o")
|
||
(("PKG_LIBS = ./liblzma.a")
|
||
"PKG_LIBS = -llz4"))
|
||
(substitute* "src/CoreArray/dStream.h"
|
||
(("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
|
||
(string-append "include <" header ">")))
|
||
#t))))
|
||
(properties `((upstream-name . "gdsfmt")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
`(("lz4" ,lz4)
|
||
("xz" ,xz)
|
||
("zlib" ,zlib)))
|
||
(home-page "http://corearray.sourceforge.net/")
|
||
(synopsis
|
||
"R Interface to CoreArray Genomic Data Structure (GDS) Files")
|
||
(description
|
||
"This package provides a high-level R interface to CoreArray @dfn{Genomic
|
||
Data Structure} (GDS) data files, which are portable across platforms with
|
||
hierarchical structure to store multiple scalable array-oriented data sets
|
||
with metadata information. It is suited for large-scale datasets, especially
|
||
for data which are much larger than the available random-access memory. The
|
||
@code{gdsfmt} package offers efficient operations specifically designed for
|
||
integers of less than 8 bits, since a diploid genotype, like
|
||
@dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
|
||
byte. Data compression and decompression are available with relatively
|
||
efficient random access. It is also allowed to read a GDS file in parallel
|
||
with multiple R processes supported by the package @code{parallel}.")
|
||
(license license:lgpl3)))
|
||
|
||
(define-public r-bigmelon
|
||
(package
|
||
(name "r-bigmelon")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "bigmelon" version))
|
||
(sha256
|
||
(base32
|
||
"0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
|
||
(properties `((upstream-name . "bigmelon")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-gdsfmt" ,r-gdsfmt)
|
||
("r-geoquery" ,r-geoquery)
|
||
("r-methylumi" ,r-methylumi)
|
||
("r-minfi" ,r-minfi)
|
||
("r-watermelon" ,r-watermelon)))
|
||
(home-page "https://bioconductor.org/packages/bigmelon/")
|
||
(synopsis "Illumina methylation array analysis for large experiments")
|
||
(description
|
||
"This package provides methods for working with Illumina arrays using the
|
||
@code{gdsfmt} package.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-seqbias
|
||
(package
|
||
(name "r-seqbias")
|
||
(version "1.32.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "seqbias" version))
|
||
(sha256
|
||
(base32
|
||
"1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw"))))
|
||
(properties `((upstream-name . "seqbias")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biostrings" ,r-biostrings)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-rhtslib" ,r-rhtslib)))
|
||
(inputs
|
||
`(("zlib" ,zlib))) ; This comes from rhtslib.
|
||
(home-page "https://bioconductor.org/packages/seqbias/")
|
||
(synopsis "Estimation of per-position bias in high-throughput sequencing data")
|
||
(description
|
||
"This package implements a model of per-position sequencing bias in
|
||
high-throughput sequencing data using a simple Bayesian network, the structure
|
||
and parameters of which are trained on a set of aligned reads and a reference
|
||
genome sequence.")
|
||
(license license:lgpl3)))
|
||
|
||
(define-public r-reqon
|
||
(package
|
||
(name "r-reqon")
|
||
(version "1.30.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ReQON" version))
|
||
(sha256
|
||
(base32
|
||
"04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a"))))
|
||
(properties `((upstream-name . "ReQON")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-rjava" ,r-rjava)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-seqbias" ,r-seqbias)))
|
||
(home-page "https://bioconductor.org/packages/ReQON/")
|
||
(synopsis "Recalibrating quality of nucleotides")
|
||
(description
|
||
"This package provides an implementation of an algorithm for
|
||
recalibrating the base quality scores for aligned sequencing data in BAM
|
||
format.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-wavcluster
|
||
(package
|
||
(name "r-wavcluster")
|
||
(version "2.18.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "wavClusteR" version))
|
||
(sha256
|
||
(base32
|
||
"02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2"))))
|
||
(properties `((upstream-name . "wavClusteR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-foreach" ,r-foreach)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-hmisc" ,r-hmisc)
|
||
("r-iranges" ,r-iranges)
|
||
("r-mclust" ,r-mclust)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-seqinr" ,r-seqinr)
|
||
("r-stringr" ,r-stringr)
|
||
("r-wmtsa" ,r-wmtsa)))
|
||
(home-page "https://bioconductor.org/packages/wavClusteR/")
|
||
(synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
|
||
(description
|
||
"This package provides an integrated pipeline for the analysis of
|
||
PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
|
||
sequencing errors, SNPs and additional non-experimental sources by a non-
|
||
parametric mixture model. The protein binding sites (clusters) are then
|
||
resolved at high resolution and cluster statistics are estimated using a
|
||
rigorous Bayesian framework. Post-processing of the results, data export for
|
||
UCSC genome browser visualization and motif search analysis are provided. In
|
||
addition, the package allows to integrate RNA-Seq data to estimate the False
|
||
Discovery Rate of cluster detection. Key functions support parallel multicore
|
||
computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
|
||
be applied to the analysis of other NGS data obtained from experimental
|
||
procedures that induce nucleotide substitutions (e.g. BisSeq).")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-timeseriesexperiment
|
||
(package
|
||
(name "r-timeseriesexperiment")
|
||
(version "1.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "TimeSeriesExperiment" version))
|
||
(sha256
|
||
(base32
|
||
"1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y"))))
|
||
(properties
|
||
`((upstream-name . "TimeSeriesExperiment")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-deseq2" ,r-deseq2)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-dynamictreecut" ,r-dynamictreecut)
|
||
("r-edger" ,r-edger)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-hmisc" ,r-hmisc)
|
||
("r-limma" ,r-limma)
|
||
("r-magrittr" ,r-magrittr)
|
||
("r-proxy" ,r-proxy)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-tibble" ,r-tibble)
|
||
("r-tidyr" ,r-tidyr)
|
||
("r-vegan" ,r-vegan)
|
||
("r-viridis" ,r-viridis)))
|
||
(home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
|
||
(synopsis "Analysis for short time-series data")
|
||
(description
|
||
"This package is a visualization and analysis toolbox for short time
|
||
course data which includes dimensionality reduction, clustering, two-sample
|
||
differential expression testing and gene ranking techniques. The package also
|
||
provides methods for retrieving enriched pathways.")
|
||
(license license:lgpl3+)))
|
||
|
||
(define-public r-variantfiltering
|
||
(package
|
||
(name "r-variantfiltering")
|
||
(version "1.20.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "VariantFiltering" version))
|
||
(sha256
|
||
(base32
|
||
"0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17"))))
|
||
(properties
|
||
`((upstream-name . "VariantFiltering")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-dt" ,r-dt)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-genomicscores" ,r-genomicscores)
|
||
("r-graph" ,r-graph)
|
||
("r-gviz" ,r-gviz)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rbgl" ,r-rbgl)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-shiny" ,r-shiny)
|
||
("r-shinyjs" ,r-shinyjs)
|
||
("r-shinythemes" ,r-shinythemes)
|
||
("r-shinytree" ,r-shinytree)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-variantannotation" ,r-variantannotation)
|
||
("r-xvector" ,r-xvector)))
|
||
(home-page "https://github.com/rcastelo/VariantFiltering")
|
||
(synopsis "Filtering of coding and non-coding genetic variants")
|
||
(description
|
||
"Filter genetic variants using different criteria such as inheritance
|
||
model, amino acid change consequence, minor allele frequencies across human
|
||
populations, splice site strength, conservation, etc.")
|
||
(license license:artistic2.0)))
|