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branch master updated: gnu: Add r-msigdb.
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guix-commits |
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branch master updated: gnu: Add r-msigdb. |
Date: |
Mon, 28 Aug 2023 04:07:00 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 0b0e050415 gnu: Add r-msigdb.
0b0e050415 is described below
commit 0b0e050415a0fe653a1f901c2c323b6d7c264d52
Author: Navid Afkhami <navid.afkhami@mdc-berlin.de>
AuthorDate: Thu Aug 24 10:38:37 2023 +0000
gnu: Add r-msigdb.
* gnu/packages/bioconductor.scm (r-msigdb): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++
1 file changed, 32 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 74071900a3..8b4f88e708 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1754,6 +1754,38 @@ LC-MSMS and MRM files from proteomics experiments; and
PSI mzIdentML example
files for various search engines.")
(license license:gpl2+)))
+(define-public r-msigdb
+ (package
+ (name "r-msigdb")
+ (version "1.8.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "msigdb" version
+ 'experiment))
+ (sha256
+ (base32
+ "1kgsqg1d5r852qas09g6fs0pcmk6jgbb6g983v6iqw19qsiy6jby"))))
+ (properties `((upstream-name . "msigdb")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-annotationdbi
+ r-annotationhub
+ r-experimenthub
+ r-gseabase
+ r-org-hs-eg-db
+ r-org-mm-eg-db))
+ (native-inputs (list r-knitr))
+ (home-page "https://doi.org/doi:10.18129/B9.bioc.msigdb")
+ (synopsis "ExperimentHub package for the molecular signatures database")
+ (description
+ "R-msigdb provides the Molecular Signatures Database in a R accessible
+objects. Signatures are stored in @code{GeneSet} class objects form the
+GSEABase package and the entire database is stored in a
+@code{GeneSetCollection} object. These data are then hosted on the
+@code{ExperimentHub}. Data used in this package was obtained from the
+@code{MSigDB} of the Broad Institute. Metadata for each gene set is stored
+along with the gene set in the @code{GeneSet} class object.")
+ (license license:cc-by4.0)))
+
(define-public r-pasilla
(package
(name "r-pasilla")
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