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authorRicardo Wurmus <rekado@elephly.net>2019-03-25 16:09:16 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-03-25 16:09:16 +0100
commitc538bcdd38ca12fbdf02b220a371ac16448cab8c (patch)
tree4403dc4193b9db098375d5871dbd035ac680f92c /gnu/packages
parent8a5460b4fb32962e835ec08907210f6416e53582 (diff)
downloadpatches-c538bcdd38ca12fbdf02b220a371ac16448cab8c.tar
patches-c538bcdd38ca12fbdf02b220a371ac16448cab8c.tar.gz
gnu: Add r-varianttools.
* gnu/packages/bioconductor.scm (r-varianttools): New variable.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioconductor.scm40
1 files changed, 40 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7bd126b5c0..744fc8780d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2579,3 +2579,43 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
distributions of TF ChIP sequencing reads, taking advantage of an improved
peak definition in combination with known profile characteristics.")
(license license:gpl2)))
+
+(define-public r-varianttools
+ (package
+ (name "r-varianttools")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "VariantTools" version))
+ (sha256
+ (base32
+ "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
+ (properties `((upstream-name . "VariantTools")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/VariantTools/")
+ (synopsis "Tools for exploratory analysis of variant calls")
+ (description
+ "Explore, diagnose, and compare variant calls using filters. The
+VariantTools package supports a workflow for loading data, calling single
+sample variants and tumor-specific somatic mutations or other sample-specific
+variant types (e.g., RNA editing). Most of the functions operate on
+alignments (BAM files) or datasets of called variants. The user is expected
+to have already aligned the reads with a separate tool, e.g., GSNAP via
+gmapR.")
+ (license license:artistic2.0)))