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authorRicardo Wurmus <rekado@elephly.net>2023-03-30 14:26:40 +0200
committerRicardo Wurmus <rekado@elephly.net>2023-03-30 14:26:40 +0200
commit96e81b18b9dd6a7fdc2d178ee8d1542f8d55826f (patch)
treecff3b5dd55eda62ce66fe6230f0b39dba58a9b9c
parent418811783ee1f3455d6394f17ffe5e221eca5e0f (diff)
downloadguix-96e81b18b9dd6a7fdc2d178ee8d1542f8d55826f.tar.gz
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gnu: Add r-champ.
* gnu/packages/bioconductor.scm (r-champ): New variable.
-rw-r--r--gnu/packages/bioconductor.scm62
1 files changed, 62 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b61fcaa051..5a59ab86eb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5900,6 +5900,68 @@ genome data packages and support for efficient SNP representation.")
analysis.")
(license license:artistic2.0)))
+(define-public r-champ
+ (package
+ (name "r-champ")
+ (version "2.28.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ChAMP" version))
+ (sha256
+ (base32
+ "10ss0a3miqrx92vy1r1h5rv3mnjn4iyl32q86s0x59d3fvqp2cx1"))))
+ (properties `((upstream-name . "ChAMP")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-bumphunter
+ r-champdata
+ r-combinat
+ r-dendextend
+ r-dmrcate
+ r-dnacopy
+ r-doparallel
+ r-dt
+ r-genomicranges
+ r-ggplot2
+ r-globaltest
+ r-goseq
+ r-hmisc
+ r-illumina450probevariants-db
+ r-illuminahumanmethylation450kmanifest
+ r-illuminahumanmethylationepicanno-ilm10b4-hg19
+ r-illuminahumanmethylationepicmanifest
+ r-illuminaio
+ r-impute
+ r-isva
+ r-kpmt
+ r-limma
+ r-marray
+ r-matrixstats
+ r-minfi
+ r-missmethyl
+ r-plotly
+ r-plyr
+ r-preprocesscore
+ r-prettydoc
+ r-quadprog
+ r-qvalue
+ r-rcolorbrewer
+ r-rmarkdown
+ r-rpmm
+ r-shiny
+ r-shinythemes
+ r-sva
+ r-watermelon))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/ChAMP")
+ (synopsis
+ "Chip analysis methylation pipeline for Illumina HumanMethylation450 and EPIC")
+ (description
+ "The package includes quality control metrics, a selection of
+normalization methods and novel methods to identify differentially methylated
+regions and to highlight copy number alterations.")
+ (license license:gpl3)))
+
(define-public r-chipseeker
(package
(name "r-chipseeker")