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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-05-10 13:04:56 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-05-10 13:31:03 +0200 |
| commit | 144415391344ca7118268889867a00a5e5b5b466 (patch) | |
| tree | 7230428ba1e747b0612f0474d134118650529cb4 /gnu | |
| parent | 30f1029f4c512e3f8ffc6eccd83ce1653eaf5d6c (diff) | |
| download | patches-144415391344ca7118268889867a00a5e5b5b466.tar patches-144415391344ca7118268889867a00a5e5b5b466.tar.gz | |
gnu: Add r-sgseq.
* gnu/packages/bioconductor.scm (r-sgseq): New variable.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c594621069..fce157a516 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4392,3 +4392,44 @@ Gaussian distributions.") aligner and around SpliceMap, a de novo splice junction discovery and alignment tool.") (license license:artistic2.0))) + +(define-public r-sgseq + (package + (name "r-sgseq") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SGSeq" version)) + (sha256 + (base32 + "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s")))) + (properties `((upstream-name . "SGSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-runit" ,r-runit) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/SGSeq/") + (synopsis "Splice event prediction and quantification from RNA-seq data") + (description + "SGSeq is a package for analyzing splice events from RNA-seq data. Input +data are RNA-seq reads mapped to a reference genome in BAM format. Genes are +represented as a splice graph, which can be obtained from existing annotation +or predicted from the mapped sequence reads. Splice events are identified +from the graph and are quantified locally using structurally compatible reads +at the start or end of each splice variant. The software includes functions +for splice event prediction, quantification, visualization and +interpretation.") + (license license:artistic2.0))) |