gnu: Add r-varianttools.
* gnu/packages/bioconductor.scm (r-varianttools): New variable.
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@ -2579,3 +2579,43 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
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distributions of TF ChIP sequencing reads, taking advantage of an improved
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peak definition in combination with known profile characteristics.")
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(license license:gpl2)))
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(define-public r-varianttools
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(package
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(name "r-varianttools")
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(version "1.24.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "VariantTools" version))
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(sha256
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(base32
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"1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
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(properties `((upstream-name . "VariantTools")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-biobase" ,r-biobase)
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("r-biocgenerics" ,r-biocgenerics)
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("r-biocparallel" ,r-biocparallel)
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("r-biostrings" ,r-biostrings)
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("r-bsgenome" ,r-bsgenome)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicfeatures" ,r-genomicfeatures)
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("r-genomicranges" ,r-genomicranges)
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("r-iranges" ,r-iranges)
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("r-matrix" ,r-matrix)
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("r-rsamtools" ,r-rsamtools)
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("r-rtracklayer" ,r-rtracklayer)
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("r-s4vectors" ,r-s4vectors)
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("r-variantannotation" ,r-variantannotation)))
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(home-page "https://bioconductor.org/packages/VariantTools/")
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(synopsis "Tools for exploratory analysis of variant calls")
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(description
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"Explore, diagnose, and compare variant calls using filters. The
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VariantTools package supports a workflow for loading data, calling single
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sample variants and tumor-specific somatic mutations or other sample-specific
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variant types (e.g., RNA editing). Most of the functions operate on
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alignments (BAM files) or datasets of called variants. The user is expected
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to have already aligned the reads with a separate tool, e.g., GSNAP via
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gmapR.")
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(license license:artistic2.0)))
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