Navid Afkhami wrote 2 years ago
(address . guix-patches@gnu.org)(name . Navid Afkhami)(address . navid.afkhami@mdc-berlin.de)
0e1abe23554c0125ec623d0926c7eb7d274c38f0.1692873517.git.navid.afkhami@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-msigdb): New variable.
---
gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
Toggle diff (48 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 74071900a3..5e323d11ef 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1754,6 +1754,39 @@ (define-public r-msdata
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://davislaboratory.github.io/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")
base-commit: 160f78a4d92205df986ed9efcce7d3aac188cb24
--
2.34.1