diff options
| -rw-r--r-- | gnu/packages/bioconductor.scm | 33 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 31 |
2 files changed, 32 insertions, 32 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28e8810bbc..a0ee8a8c18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> -;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> @@ -2499,6 +2499,37 @@ formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.") (license license:lgpl2.0+))) +(define-public r-gage + (package + (name "r-gage") + (version "2.40.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gage" version)) + (sha256 + (base32 + "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) + ("r-keggrest" ,r-keggrest))) + (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" + "articles/10.1186/1471-2105-10-161")) + (synopsis "Generally applicable gene-set enrichment for pathway analysis") + (description + "GAGE is a published method for gene set (enrichment or GSEA) or pathway +analysis. GAGE is generally applicable independent of microarray or RNA-Seq +data attributes including sample sizes, experimental designs, assay platforms, +and other types of heterogeneity. The gage package provides functions for +basic GAGE analysis, result processing and presentation. In addition, it +provides demo microarray data and commonly used gene set data based on KEGG +pathways and GO terms. These functions and data are also useful for gene set +analysis using other methods.") + (license license:gpl2+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8188b50ad6..a857c1ccc5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9168,37 +9168,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-gage - (package - (name "r-gage") - (version "2.40.2") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gage" version)) - (sha256 - (base32 - "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-keggrest" ,r-keggrest))) - (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" - "articles/10.1186/1471-2105-10-161")) - (synopsis "Generally applicable gene-set enrichment for pathway analysis") - (description - "GAGE is a published method for gene set (enrichment or GSEA) or pathway -analysis. GAGE is generally applicable independent of microarray or RNA-Seq -data attributes including sample sizes, experimental designs, assay platforms, -and other types of heterogeneity. The gage package provides functions for -basic GAGE analysis, result processing and presentation. In addition, it -provides demo microarray data and commonly used gene set data based on KEGG -pathways and GO terms. These functions and data are also useful for gene set -analysis using other methods.") - (license license:gpl2+))) - (define-public r-genomicfiles (package (name "r-genomicfiles") |