1070 lines
40 KiB
Scheme
1070 lines
40 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
|
||
;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
|
||
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
|
||
;;;
|
||
;;; This file is part of GNU Guix.
|
||
;;;
|
||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||
;;; under the terms of the GNU General Public License as published by
|
||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||
;;; your option) any later version.
|
||
;;;
|
||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||
;;; GNU General Public License for more details.
|
||
;;;
|
||
;;; You should have received a copy of the GNU General Public License
|
||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||
|
||
(define-module (gnu packages bioconductor)
|
||
#:use-module ((guix licenses) #:prefix license:)
|
||
#:use-module (guix packages)
|
||
#:use-module (guix download)
|
||
#:use-module (guix build-system r)
|
||
#:use-module (gnu packages)
|
||
#:use-module (gnu packages bioinformatics)
|
||
#:use-module (gnu packages cran)
|
||
#:use-module (gnu packages compression)
|
||
#:use-module (gnu packages graph)
|
||
#:use-module (gnu packages maths)
|
||
#:use-module (gnu packages statistics)
|
||
#:use-module (gnu packages web))
|
||
|
||
(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-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-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-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-genelendatabase
|
||
(package
|
||
(name "r-genelendatabase")
|
||
(version "1.16.0")
|
||
(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
|
||
"07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5"))))
|
||
(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-hpar
|
||
(package
|
||
(name "r-hpar")
|
||
(version "1.24.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "hpar" version))
|
||
(sha256
|
||
(base32
|
||
"1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://bioconductor.org/packages/hpar/")
|
||
(synopsis "Human Protein Atlas in R")
|
||
(description "This package provides a simple interface to and data from
|
||
the Human Protein Atlas project.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-regioner
|
||
(package
|
||
(name "r-regioner")
|
||
(version "1.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "regioneR" version))
|
||
(sha256
|
||
(base32
|
||
"19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
|
||
(properties `((upstream-name . "regioneR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biostrings" ,r-biostrings)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-memoise" ,r-memoise)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/regioneR/")
|
||
(synopsis "Association analysis of genomic regions")
|
||
(description "This package offers a statistical framework based on
|
||
customizable permutation tests to assess the association between genomic
|
||
region sets and other genomic features.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-diffbind
|
||
(package
|
||
(name "r-diffbind")
|
||
(version "2.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DiffBind" version))
|
||
(sha256
|
||
(base32
|
||
"0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
|
||
(properties `((upstream-name . "DiffBind")))
|
||
(build-system r-build-system)
|
||
(inputs
|
||
`(("zlib" ,zlib)))
|
||
(propagated-inputs
|
||
`(("r-amap" ,r-amap)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-deseq2" ,r-deseq2)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-edger" ,r-edger)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-ggrepel" ,r-ggrepel)
|
||
("r-gplots" ,r-gplots)
|
||
("r-iranges" ,r-iranges)
|
||
("r-lattice" ,r-lattice)
|
||
("r-limma" ,r-limma)
|
||
("r-locfit" ,r-locfit)
|
||
("r-rcolorbrewer" , r-rcolorbrewer)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-systempiper" ,r-systempiper)
|
||
("r-zlibbioc" ,r-zlibbioc)))
|
||
(home-page "http://bioconductor.org/packages/DiffBind")
|
||
(synopsis "Differential binding analysis of ChIP-Seq peak data")
|
||
(description
|
||
"This package computes differentially bound sites from multiple
|
||
ChIP-seq experiments using affinity (quantitative) data. Also enables
|
||
occupancy (overlap) analysis and plotting functions.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-ripseeker
|
||
(package
|
||
(name "r-ripseeker")
|
||
(version "1.22.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RIPSeeker" version))
|
||
(sha256
|
||
(base32
|
||
"1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
|
||
(properties `((upstream-name . "RIPSeeker")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-s4vectors" ,r-s4vectors)
|
||
("r-iranges" ,r-iranges)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-rtracklayer" ,r-rtracklayer)))
|
||
(home-page "http://bioconductor.org/packages/RIPSeeker")
|
||
(synopsis
|
||
"Identifying protein-associated transcripts from RIP-seq experiments")
|
||
(description
|
||
"This package infers and discriminates RIP peaks from RIP-seq alignments
|
||
using two-state HMM with negative binomial emission probability. While
|
||
RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
|
||
a suite of bioinformatics tools integrated within this self-contained software
|
||
package comprehensively addressing issues ranging from post-alignments
|
||
processing to visualization and annotation.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-multtest
|
||
(package
|
||
(name "r-multtest")
|
||
(version "2.38.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "multtest" version))
|
||
(sha256
|
||
(base32
|
||
"0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-survival" ,r-survival)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biobase" ,r-biobase)
|
||
("r-mass" ,r-mass)))
|
||
(home-page "http://bioconductor.org/packages/multtest")
|
||
(synopsis "Resampling-based multiple hypothesis testing")
|
||
(description
|
||
"This package can do non-parametric bootstrap and permutation
|
||
resampling-based multiple testing procedures (including empirical Bayes
|
||
methods) for controlling the family-wise error rate (FWER), generalized
|
||
family-wise error rate (gFWER), tail probability of the proportion of
|
||
false positives (TPPFP), and false discovery rate (FDR). Several choices
|
||
of bootstrap-based null distribution are implemented (centered, centered
|
||
and scaled, quantile-transformed). Single-step and step-wise methods are
|
||
available. Tests based on a variety of T- and F-statistics (including
|
||
T-statistics based on regression parameters from linear and survival models
|
||
as well as those based on correlation parameters) are included. When probing
|
||
hypotheses with T-statistics, users may also select a potentially faster null
|
||
distribution which is multivariate normal with mean zero and variance
|
||
covariance matrix derived from the vector influence function. Results are
|
||
reported in terms of adjusted P-values, confidence regions and test statistic
|
||
cutoffs. The procedures are directly applicable to identifying differentially
|
||
expressed genes in DNA microarray experiments.")
|
||
(license license:lgpl3)))
|
||
|
||
(define-public r-graph
|
||
(package
|
||
(name "r-graph")
|
||
(version "1.60.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "graph" version))
|
||
(sha256
|
||
(base32
|
||
"1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)))
|
||
(home-page "https://bioconductor.org/packages/graph")
|
||
(synopsis "Handle graph data structures in R")
|
||
(description
|
||
"This package implements some simple graph handling capabilities for R.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-codedepends
|
||
(package
|
||
(name "r-codedepends")
|
||
(version "0.6.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "CodeDepends" version))
|
||
(sha256
|
||
(base32
|
||
"0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
|
||
(properties `((upstream-name . "CodeDepends")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-codetools" ,r-codetools)
|
||
("r-graph" ,r-graph)
|
||
("r-xml" ,r-xml)))
|
||
(home-page "http://cran.r-project.org/web/packages/CodeDepends")
|
||
(synopsis "Analysis of R code for reproducible research and code comprehension")
|
||
(description
|
||
"This package provides tools for analyzing R expressions or blocks of
|
||
code and determining the dependencies between them. It focuses on R scripts,
|
||
but can be used on the bodies of functions. There are many facilities
|
||
including the ability to summarize or get a high-level view of code,
|
||
determining dependencies between variables, code improvement suggestions.")
|
||
;; Any version of the GPL
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-chippeakanno
|
||
(package
|
||
(name "r-chippeakanno")
|
||
(version "3.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPpeakAnno" version))
|
||
(sha256
|
||
(base32
|
||
"09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3"))))
|
||
(properties `((upstream-name . "ChIPpeakAnno")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocmanager" ,r-biocmanager)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-delayedarray" ,r-delayedarray)
|
||
("r-go-db" ,r-go-db)
|
||
("r-biomart" ,r-biomart)
|
||
("r-bsgenome" ,r-bsgenome)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-iranges" ,r-iranges)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-annotationdbi" ,r-annotationdbi)
|
||
("r-limma" ,r-limma)
|
||
("r-multtest" ,r-multtest)
|
||
("r-rbgl" ,r-rbgl)
|
||
("r-graph" ,r-graph)
|
||
("r-regioner" ,r-regioner)
|
||
("r-dbi" ,r-dbi)
|
||
("r-ensembldb" ,r-ensembldb)
|
||
("r-biobase" ,r-biobase)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-seqinr" ,r-seqinr)
|
||
("r-idr" ,r-idr)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-venndiagram" ,r-venndiagram)))
|
||
(home-page "http://bioconductor.org/packages/ChIPpeakAnno")
|
||
(synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
|
||
(description
|
||
"The package includes functions to retrieve the sequences around the peak,
|
||
obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
|
||
custom features such as most conserved elements and other transcription factor
|
||
binding sites supplied by users. Starting 2.0.5, new functions have been added
|
||
for finding the peaks with bi-directional promoters with summary statistics
|
||
(peaksNearBDP), for summarizing the occurrence of motifs in peaks
|
||
(summarizePatternInPeaks) and for adding other IDs to annotated peaks or
|
||
enrichedGO (addGeneIDs).")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-marray
|
||
(package
|
||
(name "r-marray")
|
||
(version "1.60.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "marray" version))
|
||
(sha256
|
||
(base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-limma" ,r-limma)))
|
||
(home-page "http://bioconductor.org/packages/marray")
|
||
(synopsis "Exploratory analysis for two-color spotted microarray data")
|
||
(description "This package contains class definitions for two-color spotted
|
||
microarray data. It also includes fuctions for data input, diagnostic plots,
|
||
normalization and quality checking.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-cghbase
|
||
(package
|
||
(name "r-cghbase")
|
||
(version "1.42.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "CGHbase" version))
|
||
(sha256
|
||
(base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
|
||
(properties `((upstream-name . "CGHbase")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-marray" ,r-marray)))
|
||
(home-page "http://bioconductor.org/packages/CGHbase")
|
||
(synopsis "Base functions and classes for arrayCGH data analysis")
|
||
(description "This package contains functions and classes that are needed by
|
||
the @code{arrayCGH} packages.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-cghcall
|
||
(package
|
||
(name "r-cghcall")
|
||
(version "2.44.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "CGHcall" version))
|
||
(sha256
|
||
(base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
|
||
(properties `((upstream-name . "CGHcall")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-cghbase" ,r-cghbase)
|
||
("r-impute" ,r-impute)
|
||
("r-dnacopy" ,r-dnacopy)
|
||
("r-snowfall" ,r-snowfall)))
|
||
(home-page "http://bioconductor.org/packages/CGHcall")
|
||
(synopsis "Base functions and classes for arrayCGH data analysis")
|
||
(description "This package contains functions and classes that are needed by
|
||
@code{arrayCGH} packages.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-qdnaseq
|
||
(package
|
||
(name "r-qdnaseq")
|
||
(version "1.18.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "QDNAseq" version))
|
||
(sha256
|
||
(base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
|
||
(properties `((upstream-name . "QDNAseq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-cghbase" ,r-cghbase)
|
||
("r-cghcall" ,r-cghcall)
|
||
("r-dnacopy" ,r-dnacopy)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-matrixstats" ,r-matrixstats)
|
||
("r-r-utils" ,r-r-utils)
|
||
("r-rsamtools" ,r-rsamtools)))
|
||
(home-page "http://bioconductor.org/packages/QDNAseq")
|
||
(synopsis "Quantitative DNA sequencing for chromosomal aberrations")
|
||
(description "The genome is divided into non-overlapping fixed-sized bins,
|
||
number of sequence reads in each counted, adjusted with a simultaneous
|
||
two-dimensional loess correction for sequence mappability and GC content, and
|
||
filtered to remove spurious regions in the genome. Downstream steps of
|
||
segmentation and calling are also implemented via packages DNAcopy and CGHcall,
|
||
respectively.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-bayseq
|
||
(package
|
||
(name "r-bayseq")
|
||
(version "2.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "baySeq" version))
|
||
(sha256
|
||
(base32
|
||
"0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
|
||
(properties `((upstream-name . "baySeq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-abind" ,r-abind)
|
||
("r-edger" ,r-edger)
|
||
("r-genomicranges" ,r-genomicranges)))
|
||
(home-page "https://bioconductor.org/packages/baySeq/")
|
||
(synopsis "Bayesian analysis of differential expression patterns in count data")
|
||
(description
|
||
"This package identifies differential expression in high-throughput count
|
||
data, such as that derived from next-generation sequencing machines,
|
||
calculating estimated posterior likelihoods of differential expression (or
|
||
more complex hypotheses) via empirical Bayesian methods.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-chipcomp
|
||
(package
|
||
(name "r-chipcomp")
|
||
(version "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPComp" version))
|
||
(sha256
|
||
(base32
|
||
"1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
|
||
(properties `((upstream-name . "ChIPComp")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
|
||
("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-limma" ,r-limma)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/ChIPComp")
|
||
(synopsis "Quantitative comparison of multiple ChIP-seq datasets")
|
||
(description
|
||
"ChIPComp implements a statistical method for quantitative comparison of
|
||
multiple ChIP-seq datasets. It detects differentially bound sharp binding
|
||
sites across multiple conditions considering matching control in ChIP-seq
|
||
datasets.")
|
||
;; Any version of the GPL.
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-riboprofiling
|
||
(package
|
||
(name "r-riboprofiling")
|
||
(version "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RiboProfiling" version))
|
||
(sha256
|
||
(base32
|
||
"1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
|
||
(properties `((upstream-name . "RiboProfiling")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biostrings" ,r-biostrings)
|
||
("r-data-table" ,r-data-table)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggbio" ,r-ggbio)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-iranges" ,r-iranges)
|
||
("r-plyr" ,r-plyr)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-sqldf" ,r-sqldf)))
|
||
(home-page "https://bioconductor.org/packages/RiboProfiling/")
|
||
(synopsis "Ribosome profiling data analysis")
|
||
(description "Starting with a BAM file, this package provides the
|
||
necessary functions for quality assessment, read start position recalibration,
|
||
the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
|
||
of count data: pairs, log fold-change, codon frequency and coverage
|
||
assessment, principal component analysis on codon coverage.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-riboseqr
|
||
(package
|
||
(name "r-riboseqr")
|
||
(version "1.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "riboSeqR" version))
|
||
(sha256
|
||
(base32
|
||
"1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
|
||
(properties `((upstream-name . "riboSeqR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-abind" ,r-abind)
|
||
("r-bayseq" ,r-bayseq)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-seqlogo" ,r-seqlogo)))
|
||
(home-page "https://bioconductor.org/packages/riboSeqR/")
|
||
(synopsis "Analysis of sequencing data from ribosome profiling experiments")
|
||
(description
|
||
"This package provides plotting functions, frameshift detection and
|
||
parsing of genetic sequencing data from ribosome profiling experiments.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-interactionset
|
||
(package
|
||
(name "r-interactionset")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "InteractionSet" version))
|
||
(sha256
|
||
(base32
|
||
"0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
|
||
(properties
|
||
`((upstream-name . "InteractionSet")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocgenerics" ,r-biocgenerics)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-matrix" ,r-matrix)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)))
|
||
(home-page "https://bioconductor.org/packages/InteractionSet")
|
||
(synopsis "Base classes for storing genomic interaction data")
|
||
(description
|
||
"This packages provides the @code{GInteractions},
|
||
@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
|
||
for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
|
||
experiments.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-genomicinteractions
|
||
(package
|
||
(name "r-genomicinteractions")
|
||
(version "1.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "GenomicInteractions" version))
|
||
(sha256
|
||
(base32
|
||
"0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
|
||
(properties
|
||
`((upstream-name . "GenomicInteractions")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-data-table" ,r-data-table)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-gviz" ,r-gviz)
|
||
("r-igraph" ,r-igraph)
|
||
("r-interactionset" ,r-interactionset)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-rtracklayer" ,r-rtracklayer)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-stringr" ,r-stringr)))
|
||
(home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
|
||
(synopsis "R package for handling genomic interaction data")
|
||
(description
|
||
"This R package provides tools for handling genomic interaction data,
|
||
such as ChIA-PET/Hi-C, annotating genomic features with interaction
|
||
information and producing various plots and statistics.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-ctc
|
||
(package
|
||
(name "r-ctc")
|
||
(version "1.56.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ctc" version))
|
||
(sha256
|
||
(base32
|
||
"0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs `(("r-amap" ,r-amap)))
|
||
(home-page "https://bioconductor.org/packages/ctc/")
|
||
(synopsis "Cluster and tree conversion")
|
||
(description
|
||
"This package provides tools for exporting and importing classification
|
||
trees and clusters to other programs.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-goseq
|
||
(package
|
||
(name "r-goseq")
|
||
(version "1.34.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "goseq" version))
|
||
(sha256
|
||
(base32
|
||
"1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-annotationdbi" ,r-annotationdbi)
|
||
("r-biasedurn" ,r-biasedurn)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-genelendatabase" ,r-genelendatabase)
|
||
("r-go-db" ,r-go-db)
|
||
("r-mgcv" ,r-mgcv)))
|
||
(home-page "https://bioconductor.org/packages/goseq/")
|
||
(synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
|
||
(description
|
||
"This package provides tools to detect Gene Ontology and/or other user
|
||
defined categories which are over/under represented in RNA-seq data.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-glimma
|
||
(package
|
||
(name "r-glimma")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "Glimma" version))
|
||
(sha256
|
||
(base32
|
||
"0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947"))))
|
||
(properties `((upstream-name . "Glimma")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-edger" ,r-edger)
|
||
("r-jsonlite" ,r-jsonlite)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://github.com/Shians/Glimma")
|
||
(synopsis "Interactive HTML graphics")
|
||
(description
|
||
"This package generates interactive visualisations for analysis of
|
||
RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
|
||
HTML page. The interactions are built on top of the popular static
|
||
representations of analysis results in order to provide additional
|
||
information.")
|
||
(license license:lgpl3)))
|
||
|
||
(define-public r-rots
|
||
(package
|
||
(name "r-rots")
|
||
(version "1.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ROTS" version))
|
||
(sha256
|
||
(base32
|
||
"137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5"))))
|
||
(properties `((upstream-name . "ROTS")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-rcpp" ,r-rcpp)))
|
||
(home-page "https://bioconductor.org/packages/ROTS/")
|
||
(synopsis "Reproducibility-Optimized Test Statistic")
|
||
(description
|
||
"This package provides tools for calculating the
|
||
@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
|
||
in omics data.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-inspect
|
||
(package
|
||
(name "r-inspect")
|
||
(version "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "INSPEcT" version))
|
||
(sha256
|
||
(base32
|
||
"0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2"))))
|
||
(properties `((upstream-name . "INSPEcT")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-biocparallel" ,r-biocparallel)
|
||
("r-desolve" ,r-desolve)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicfeatures" ,r-genomicfeatures)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-iranges" ,r-iranges)
|
||
("r-preprocesscore" ,r-preprocesscore)
|
||
("r-proc" ,r-proc)
|
||
("r-rootsolve" ,r-rootsolve)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/INSPEcT")
|
||
(synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
|
||
(description
|
||
"INSPEcT (INference of Synthesis, Processing and dEgradation rates in
|
||
Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
|
||
order to evaluate synthesis, processing and degradation rates and assess via
|
||
modeling the rates that determines changes in mature mRNA levels.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-dnabarcodes
|
||
(package
|
||
(name "r-dnabarcodes")
|
||
(version "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "DNABarcodes" version))
|
||
(sha256
|
||
(base32
|
||
"0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
|
||
(properties `((upstream-name . "DNABarcodes")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-bh" ,r-bh)
|
||
("r-matrix" ,r-matrix)
|
||
("r-rcpp" ,r-rcpp)))
|
||
(home-page "https://bioconductor.org/packages/DNABarcodes")
|
||
(synopsis "Create and analyze DNA barcodes")
|
||
(description
|
||
"This package offers tools to create DNA barcode sets capable of
|
||
correcting insertion, deletion, and substitution errors. Existing barcodes
|
||
can be analyzed regarding their minimal, maximal and average distances between
|
||
barcodes. Finally, reads that start with a (possibly mutated) barcode can be
|
||
demultiplexed, i.e. assigned to their original reference barcode.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-ruvseq
|
||
(package
|
||
(name "r-ruvseq")
|
||
(version "1.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "RUVSeq" version))
|
||
(sha256
|
||
(base32
|
||
"0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m"))))
|
||
(properties `((upstream-name . "RUVSeq")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-edaseq" ,r-edaseq)
|
||
("r-edger" ,r-edger)
|
||
("r-mass" ,r-mass)))
|
||
(home-page "https://github.com/drisso/RUVSeq")
|
||
(synopsis "Remove unwanted variation from RNA-Seq data")
|
||
(description
|
||
"This package implements methods to @dfn{remove unwanted variation} (RUV)
|
||
of Risso et al. (2014) for the normalization of RNA-Seq read counts between
|
||
samples.")
|
||
(license license:artistic2.0)))
|
||
|
||
(define-public r-biocneighbors
|
||
(package
|
||
(name "r-biocneighbors")
|
||
(version "1.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "BiocNeighbors" version))
|
||
(sha256
|
||
(base32
|
||
"1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
|
||
(properties `((upstream-name . "BiocNeighbors")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocparallel" ,r-biocparallel)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rcppannoy" ,r-rcppannoy)
|
||
("r-s4vectors" ,r-s4vectors)))
|
||
(home-page "https://bioconductor.org/packages/BiocNeighbors")
|
||
(synopsis "Nearest Neighbor Detection for Bioconductor packages")
|
||
(description
|
||
"This package implements exact and approximate methods for nearest
|
||
neighbor detection, in a framework that allows them to be easily switched
|
||
within Bioconductor packages or workflows. The exact algorithm is implemented
|
||
using pre-clustering with the k-means algorithm. Functions are also provided
|
||
to search for all neighbors within a given distance. Parallelization is
|
||
achieved for all methods using the BiocParallel framework.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-destiny
|
||
(package
|
||
(name "r-destiny")
|
||
(version "2.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "destiny" version))
|
||
(sha256
|
||
(base32
|
||
"1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biobase" ,r-biobase)
|
||
("r-biocgenerics" ,r-biocgenerics)
|
||
("r-fnn" ,r-fnn)
|
||
("r-ggthemes" ,r-ggthemes)
|
||
("r-hmisc" ,r-hmisc)
|
||
("r-igraph" ,r-igraph)
|
||
("r-matrix" ,r-matrix)
|
||
("r-proxy" ,r-proxy)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rcppeigen" ,r-rcppeigen)
|
||
("r-scales" ,r-scales)
|
||
("r-scatterplot3d" ,r-scatterplot3d)
|
||
("r-smoother" ,r-smoother)
|
||
("r-summarizedexperiment" ,r-summarizedexperiment)
|
||
("r-vim" ,r-vim)))
|
||
(home-page "https://bioconductor.org/packages/destiny/")
|
||
(synopsis "Create and plot diffusion maps")
|
||
(description "This package provides tools to create and plot diffusion
|
||
maps.")
|
||
;; Any version of the GPL
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-savr
|
||
(package
|
||
(name "r-savr")
|
||
(version "1.20.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "savR" version))
|
||
(sha256
|
||
(base32
|
||
"13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
|
||
(properties `((upstream-name . "savR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-ggplot2" ,r-ggplot2)
|
||
("r-gridextra" ,r-gridextra)
|
||
("r-reshape2" ,r-reshape2)
|
||
("r-scales" ,r-scales)
|
||
("r-xml" ,r-xml)))
|
||
(home-page "https://github.com/bcalder/savR")
|
||
(synopsis "Parse and analyze Illumina SAV files")
|
||
(description
|
||
"This package provides tools to parse Illumina Sequence Analysis
|
||
Viewer (SAV) files, access data, and generate QC plots.")
|
||
(license license:agpl3+)))
|
||
|
||
(define-public r-chipexoqual
|
||
(package
|
||
(name "r-chipexoqual")
|
||
(version "1.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (bioconductor-uri "ChIPexoQual" version))
|
||
(sha256
|
||
(base32
|
||
"1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
|
||
(properties `((upstream-name . "ChIPexoQual")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
`(("r-biocparallel" ,r-biocparallel)
|
||
("r-biovizbase" ,r-biovizbase)
|
||
("r-broom" ,r-broom)
|
||
("r-data-table" ,r-data-table)
|
||
("r-dplyr" ,r-dplyr)
|
||
("r-genomeinfodb" ,r-genomeinfodb)
|
||
("r-genomicalignments" ,r-genomicalignments)
|
||
("r-genomicranges" ,r-genomicranges)
|
||
("r-ggplot2" ,r-ggplot2)
|
||
("r-hexbin" ,r-hexbin)
|
||
("r-iranges" ,r-iranges)
|
||
("r-rcolorbrewer" ,r-rcolorbrewer)
|
||
("r-rmarkdown" ,r-rmarkdown)
|
||
("r-rsamtools" ,r-rsamtools)
|
||
("r-s4vectors" ,r-s4vectors)
|
||
("r-scales" ,r-scales)
|
||
("r-viridis" ,r-viridis)))
|
||
(home-page "https://github.com/keleslab/ChIPexoQual")
|
||
(synopsis "Quality control pipeline for ChIP-exo/nexus data")
|
||
(description
|
||
"This package provides a quality control pipeline for ChIP-exo/nexus
|
||
sequencing data.")
|
||
(license license:gpl2+)))
|