gnu: Add r-varianttools.

* gnu/packages/bioconductor.scm (r-varianttools): New variable.
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Ricardo Wurmus 2019-03-25 16:09:16 +01:00
parent 8a5460b4fb
commit c538bcdd38
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@ -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)))