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gnu: Add r-sgseq.
* gnu/packages/bioconductor.scm (r-sgseq): New variable.
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@ -4392,3 +4392,44 @@ (define-public r-rbowtie
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aligner and around SpliceMap, a de novo splice junction discovery and
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alignment tool.")
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(license license:artistic2.0)))
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(define-public r-sgseq
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(package
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(name "r-sgseq")
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(version "1.18.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "SGSeq" version))
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(sha256
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(base32
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"09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
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(properties `((upstream-name . "SGSeq")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-annotationdbi" ,r-annotationdbi)
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("r-biocgenerics" ,r-biocgenerics)
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("r-biostrings" ,r-biostrings)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicalignments" ,r-genomicalignments)
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("r-genomicfeatures" ,r-genomicfeatures)
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("r-genomicranges" ,r-genomicranges)
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("r-igraph" ,r-igraph)
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("r-iranges" ,r-iranges)
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("r-rsamtools" ,r-rsamtools)
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("r-rtracklayer" ,r-rtracklayer)
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("r-runit" ,r-runit)
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("r-s4vectors" ,r-s4vectors)
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("r-summarizedexperiment" ,r-summarizedexperiment)))
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(home-page "https://bioconductor.org/packages/SGSeq/")
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(synopsis "Splice event prediction and quantification from RNA-seq data")
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(description
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"SGSeq is a package for analyzing splice events from RNA-seq data. Input
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data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
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represented as a splice graph, which can be obtained from existing annotation
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or predicted from the mapped sequence reads. Splice events are identified
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from the graph and are quantified locally using structurally compatible reads
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at the start or end of each splice variant. The software includes functions
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for splice event prediction, quantification, visualization and
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interpretation.")
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(license license:artistic2.0)))
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