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gnu: r-gage: Move to (gnu packages bioconductor).

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* gnu/packages/bioinformatics.scm (r-gage): Move from here...
* gnu/packages/bioconductor.scm (r-gage): ...to here.
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zimoun 2021-05-21 22:25:56 +02:00 committed by Ricardo Wurmus
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commit 84019edf38
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2 changed files with 32 additions and 32 deletions
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33
gnu/packages/bioconductor.scm
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@ -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")

31
gnu/packages/bioinformatics.scm
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@ -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")