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authorRicardo Wurmus <rekado@elephly.net>2017-08-17 17:59:20 +0200
committerRicardo Wurmus <rekado@elephly.net>2017-08-17 18:00:17 +0200
commitbf3fa996543686cea4373d66b040a5991e4bb605 (patch)
treebf749d3f7c44199076dec32ff3c576f543cc0f4e /gnu
parent8a39e4a553ba1fff6673e73ff84d2c12d874d026 (diff)
downloadgnu-guix-bf3fa996543686cea4373d66b040a5991e4bb605.tar
gnu-guix-bf3fa996543686cea4373d66b040a5991e4bb605.tar.gz
gnu: Add r-methylkit.
* gnu/packages/bioinformatics.scm (r-methylkit): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm46
1 files changed, 46 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2728d7a26e..018a262129 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8668,6 +8668,52 @@ CopywriteR constitutes a widely applicable alternative to available copy
number detection tools.")
(license license:gpl2)))
+(define-public r-methylkit
+ (package
+ (name "r-methylkit")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "methylKit" version))
+ (sha256
+ (base32
+ "02acdjf6jl0c1glymin84pdna4farn4vv0gb6107d9iqz3y3gkmm"))))
+ (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-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)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://code.google.com/p/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-sva
(package
(name "r-sva")