diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 54 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 54 |
2 files changed, 54 insertions, 54 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 283ae7adf8..526c2eecbb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1888,6 +1888,60 @@ 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 "1.24.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "systemPipeR" version)) + (sha256 + (base32 + "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) + (properties `((upstream-name . "systemPipeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-assertthat" ,r-assertthat) + ("r-batchtools" ,r-batchtools) + ("r-biostrings" ,r-biostrings) + ("r-deseq2" ,r-deseq2) + ("r-dot" ,r-dot) + ("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-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-magrittr" ,r-magrittr) + ("r-pheatmap" ,r-pheatmap) + ("r-rjson" ,r-rjson) + ("r-rsamtools" ,r-rsamtools) + ("r-rsvg" ,r-rsvg) + ("r-shortread" ,r-shortread) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-yaml" ,r-yaml) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (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 r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f363d64550..b2d10457fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,60 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-systempiper - (package - (name "r-systempiper") - (version "1.24.3") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "systemPipeR" version)) - (sha256 - (base32 - "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) - (properties `((upstream-name . "systemPipeR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-assertthat" ,r-assertthat) - ("r-batchtools" ,r-batchtools) - ("r-biostrings" ,r-biostrings) - ("r-deseq2" ,r-deseq2) - ("r-dot" ,r-dot) - ("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-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-pheatmap" ,r-pheatmap) - ("r-rjson" ,r-rjson) - ("r-rsamtools" ,r-rsamtools) - ("r-rsvg" ,r-rsvg) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-yaml" ,r-yaml) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (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 r-grohmm (package (name "r-grohmm") |