@@ 5350,6 5350,52 @@ purposes. The package also contains legacy support for early single-end,
ungapped alignment formats.")
(license license:artistic2.0)))
+(define-public r-systempiper
+ (package
+ (name "r-systempiper")
+ (version "1.6.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "systemPipeR" version))
+ (sha256
+ (base32
+ "0s2g46a5d5bvx45i3cgmib48wf8hrniyladhm0f7kgcbfx57248m"))))
+ (properties `((upstream-name . "systemPipeR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-batchjobs" ,r-batchjobs)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-deseq2" ,r-deseq2)
+ ("r-edger" ,r-edger)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-go-db" ,r-go-db)
+ ("r-gostats" ,r-gostats)
+ ("r-limma" ,r-limma)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-rjson" ,r-rjson)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-shortread" ,r-shortread)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://github.com/tgirke/systemPipeR")
+ (synopsis "Next generation sequencing workflow and reporting environment")
+ (description
+ "This R package provides tools for building and running automated
+end-to-end analysis workflows for a wide range of @dfn{next generation
+sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
+Important features include a uniform workflow interface across different NGS
+applications, automated report generation, and support for running both R and
+command-line software, such as NGS aligners or peak/variant callers, on local
+computers or compute clusters. Efficient handling of complex sample sets and
+experimental designs is facilitated by a consistently implemented sample
+annotation infrastructure.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")