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gnu: r-methylkit: Move to (gnu packages bioconductor).

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* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
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zimoun 2021-05-21 22:26:22 +02:00 • committed by Ricardo Wurmus
parent 7ab44aeed6
commit c294c0d782
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2 changed files with 47 additions and 47 deletions
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47
gnu/packages/bioconductor.scm
View file

@ -3307,6 +3307,53 @@ and the assessment of differential expression. The analysis methods apply to
different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(license license:gpl2+)))
(define-public r-methylkit
(package
(name "r-methylkit")
(version "1.16.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "methylKit" version))
(sha256
(base32
"1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))
(properties `((upstream-name . "methylKit")))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
("r-emdbook" ,r-emdbook)
("r-fastseg" ,r-fastseg)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-gtools" ,r-gtools)
("r-iranges" ,r-iranges)
("r-kernsmooth" ,r-kernsmooth)
("r-limma" ,r-limma)
("r-mclust" ,r-mclust)
("r-mgcv" ,r-mgcv)
("r-qvalue" ,r-qvalue)
("r-r-utils" ,r-r-utils)
("r-rcpp" ,r-rcpp)
("r-rhtslib" ,r-rhtslib)
("r-rsamtools" ,r-rsamtools)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-zlibbioc" ,r-zlibbioc)))
(native-inputs
`(("r-knitr" ,r-knitr))) ; for vignettes
(home-page "https://github.com/al2na/methylKit")
(synopsis
"DNA methylation analysis from high-throughput bisulfite sequencing results")
(description
"MethylKit is an R package for DNA methylation analysis and annotation
from high-throughput bisulfite sequencing. The package is designed to deal
with sequencing data from @dfn{Reduced representation bisulfite
sequencing} (RRBS) and its variants, but also target-capture methods and whole
genome bisulfite sequencing. It also has functions to analyze base-pair
resolution 5hmC data from experimental protocols such as oxBS-Seq and
TAB-Seq.")
(license license:artistic2.0)))
(define-public r-motifrg
(package
(name "r-motifrg")

47
gnu/packages/bioinformatics.scm
View file

@ -8486,53 +8486,6 @@ analysis, variant tools is project based and provides a whole set of tools to
manipulate and analyze genetic variants.")
(license license:gpl3+)))
(define-public r-methylkit
(package
(name "r-methylkit")
(version "1.16.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "methylKit" version))
(sha256
(base32
"1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))
(properties `((upstream-name . "methylKit")))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
("r-emdbook" ,r-emdbook)
("r-fastseg" ,r-fastseg)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-gtools" ,r-gtools)
("r-iranges" ,r-iranges)
("r-kernsmooth" ,r-kernsmooth)
("r-limma" ,r-limma)
("r-mclust" ,r-mclust)
("r-mgcv" ,r-mgcv)
("r-qvalue" ,r-qvalue)
("r-r-utils" ,r-r-utils)
("r-rcpp" ,r-rcpp)
("r-rhtslib" ,r-rhtslib)
("r-rsamtools" ,r-rsamtools)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-zlibbioc" ,r-zlibbioc)))
(native-inputs
`(("r-knitr" ,r-knitr))) ; for vignettes
(home-page "https://github.com/al2na/methylKit")
(synopsis
"DNA methylation analysis from high-throughput bisulfite sequencing results")
(description
"MethylKit is an R package for DNA methylation analysis and annotation
from high-throughput bisulfite sequencing. The package is designed to deal
with sequencing data from @dfn{Reduced representation bisulfite
sequencing} (RRBS) and its variants, but also target-capture methods and whole
genome bisulfite sequencing. It also has functions to analyze base-pair
resolution 5hmC data from experimental protocols such as oxBS-Seq and
TAB-Seq.")
(license license:artistic2.0)))
(define-public r-raremetals2
(package
(name "r-raremetals2")