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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2017-01-04 16:25:21 +0100
committerRicardo Wurmus <rekado@elephly.net>2017-01-06 16:31:19 +0100
commit3a3bf2f81977a1ff4a74957753340aab57f5a12d (patch)
treeae76ceb1c38ef5f481493916188c8f3f88d05f14
parentd407bdb9318aa56ed2e0ffe520fa606a84568b01 (diff)
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patches-3a3bf2f81977a1ff4a74957753340aab57f5a12d.tar.gz
gnu: Add r-copywriter.
* gnu/packages/bioinformatics.scm (r-copywriter): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm40
1 files changed, 40 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 35269f8071..14daf59c92 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7920,3 +7920,43 @@ mm10. In addition, it contains a blacklist filter to remove regions that
display copy number variation. Files are stored as GRanges objects from the
GenomicRanges Bioconductor package.")
(license license:gpl2)))
+
+(define-public r-copywriter
+ (package
+ (name "r-copywriter")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CopywriteR" version))
+ (sha256
+ (base32
+ "1bwwnsyk7cpgwkagsnn5mv6fv233b0rkhjvbadrh70h8m4anawfj"))))
+ (properties `((upstream-name . "CopywriteR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-chipseq" ,r-chipseq)
+ ("r-copyhelper" ,r-copyhelper)
+ ("r-data-table" ,r-data-table)
+ ("r-dnacopy" ,r-dnacopy)
+ ("r-futile-logger" ,r-futile-logger)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/PeeperLab/CopywriteR")
+ (synopsis "Copy number information from targeted sequencing")
+ (description
+ "CopywriteR extracts DNA copy number information from targeted sequencing
+by utilizing off-target reads. It allows for extracting uniformly distributed
+copy number information, can be used without reference, and can be applied to
+sequencing data obtained from various techniques including chromatin
+immunoprecipitation and target enrichment on small gene panels. Thereby,
+CopywriteR constitutes a widely applicable alternative to available copy
+number detection tools.")
+ (license license:gpl2)))