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authorzimoun <zimon.toutoune@gmail.com>2021-05-21 22:25:56 +0200
committerRicardo Wurmus <rekado@elephly.net>2021-05-31 15:37:59 +0200
commit84019edf38fea7ded047464fa4a6c79675934ae4 (patch)
tree9c1a9c56f1331e10a76f8013a5eaf5b6133ff062 /gnu/packages
parentd0a5503752cab62efbaa06bd00fb92145e015732 (diff)
downloadguix-84019edf38fea7ded047464fa4a6c79675934ae4.tar.gz
guix-84019edf38fea7ded047464fa4a6c79675934ae4.zip
gnu: r-gage: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-gage): Move from here... * gnu/packages/bioconductor.scm (r-gage): ...to here.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioconductor.scm33
-rw-r--r--gnu/packages/bioinformatics.scm31
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")