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authorRicardo Wurmus <rekado@elephly.net>2019-03-13 13:35:33 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-03-13 13:35:33 +0100
commit5ec5ba027208f0028009a5e0b9b1dcb97ffe520e (patch)
tree2e9a6618b0cdfb513b693e3bbc67d62cbfd32f49 /gnu/packages
parent0f5c9cec502e0b4c8b4a8aa5b9c42474920c3e03 (diff)
downloadpatches-5ec5ba027208f0028009a5e0b9b1dcb97ffe520e.tar
patches-5ec5ba027208f0028009a5e0b9b1dcb97ffe520e.tar.gz
gnu: Add r-methylumi.
* gnu/packages/bioconductor.scm (r-methylumi): New variable.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioconductor.scm44
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 39eb705a02..c0dbbebea6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2315,3 +2315,47 @@ studies.")
"This package provides tools to analyze and visualize Illumina Infinium
methylation arrays.")
(license license:artistic2.0)))
+
+(define-public r-methylumi
+ (package
+ (name "r-methylumi")
+ (version "2.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "methylumi" version))
+ (sha256
+ (base32
+ "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
+ ("r-genefilter" ,r-genefilter)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-illuminaio" ,r-illuminaio)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-minfi" ,r-minfi)
+ ("r-reshape2" ,r-reshape2)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/methylumi")
+ (synopsis "Handle Illumina methylation data")
+ (description
+ "This package provides classes for holding and manipulating Illumina
+methylation data. Based on eSet, it can contain MIAME information, sample
+information, feature information, and multiple matrices of data. An
+\"intelligent\" import function, methylumiR can read the Illumina text files
+and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
+HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
+background correction, and quality control features for GoldenGate, Infinium,
+and Infinium HD arrays are also included.")
+ (license license:gpl2)))