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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-03-25 16:09:16 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-03-25 16:09:16 +0100 |
| commit | c538bcdd38ca12fbdf02b220a371ac16448cab8c (patch) | |
| tree | 4403dc4193b9db098375d5871dbd035ac680f92c | |
| parent | 8a5460b4fb32962e835ec08907210f6416e53582 (diff) | |
| download | patches-c538bcdd38ca12fbdf02b220a371ac16448cab8c.tar patches-c538bcdd38ca12fbdf02b220a371ac16448cab8c.tar.gz | |
gnu: Add r-varianttools.
* gnu/packages/bioconductor.scm (r-varianttools): New variable.
| -rw-r--r-- | gnu/packages/bioconductor.scm | 40 |
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))) |