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authorRoel Janssen <roel@gnu.org>2018-04-24 14:12:32 +0200
committerRoel Janssen <roel@gnu.org>2018-04-24 14:12:32 +0200
commit0ef8cc9c1c568c03c368bcaee5c3e846b8bcc9d2 (patch)
treef4487753840af9ac31fd66a610a74aa2fe87733d /gnu/packages/bioconductor.scm
parent67ee83d6c30b7b73facf1f9a7c981d05399ff190 (diff)
downloadguix-0ef8cc9c1c568c03c368bcaee5c3e846b8bcc9d2.tar
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gnu: Add r-qdnaseq.
* gnu/packages/bioconductor.scm (r-qdnaseq): New variable.
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r--gnu/packages/bioconductor.scm31
1 files changed, 31 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9b1d8667a6..76ff773ef1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -298,3 +298,34 @@ the @code{arrayCGH} packages.")
(description "This package contains functions and classes that are needed by
@code{arrayCGH} packages.")
(license license:gpl2+)))
+
+(define-public r-qdnaseq
+ (package
+ (name "r-qdnaseq")
+ (version "1.14.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "QDNAseq" version))
+ (sha256
+ (base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy"))))
+ (properties `((upstream-name . "QDNAseq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-cghbase" ,r-cghbase)
+ ("r-cghcall" ,r-cghcall)
+ ("r-dnacopy" ,r-dnacopy)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-r-utils" ,r-r-utils)
+ ("r-rsamtools" ,r-rsamtools)))
+ (home-page "http://bioconductor.org/packages/QDNAseq")
+ (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
+ (description "The genome is divided into non-overlapping fixed-sized bins,
+number of sequence reads in each counted, adjusted with a simultaneous
+two-dimensional loess correction for sequence mappability and GC content, and
+filtered to remove spurious regions in the genome. Downstream steps of
+segmentation and calling are also implemented via packages DNAcopy and CGHcall,
+respectively.")
+ (license license:gpl2+)))