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branch master updated: gnu: Add r-gsva.
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guix-commits |
Subject: |
branch master updated: gnu: Add r-gsva. |
Date: |
Wed, 19 Jul 2023 03:59:15 -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 b2750695f7 gnu: Add r-gsva.
b2750695f7 is described below
commit b2750695f72519286cb0530431396767588cc67d
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Jul 19 09:50:08 2023 +0200
gnu: Add r-gsva.
* gnu/packages/bioconductor.scm (r-gsva): New variable.
---
gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8549d2404d..4f1a4d61b1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7183,6 +7183,46 @@ testing and other simple calculations.")
Enrichment Analysis} (GSEA).")
(license license:artistic2.0)))
+(define-public r-gsva
+ (package
+ (name "r-gsva")
+ (version "1.48.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GSVA" version))
+ (sha256
+ (base32
+ "1y0dz9ayyrz4ylppa8f4m4b20yajzdl1sz4wpz8kcsfhh71ii64y"))))
+ (properties `((upstream-name . "GSVA")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biobase
+ r-biocparallel
+ r-biocsingular
+ r-delayedarray
+ r-delayedmatrixstats
+ r-gseabase
+ r-hdf5array
+ r-iranges
+ r-matrix
+ r-s4vectors
+ r-singlecellexperiment
+ r-sparsematrixstats
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/rcastelo/GSVA")
+ (synopsis "Gene Set Variation Analysis for microarray and RNA-seq data")
+ (description
+ "Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised
+method for estimating variation of gene set enrichment through the samples of
+a expression data set. GSVA performs a change in coordinate systems,
+transforming the data from a gene by sample matrix to a gene-set by sample
+matrix, thereby allowing the evaluation of pathway enrichment for each sample.
+This new matrix of GSVA enrichment scores facilitates applying standard
+analytical methods like functional enrichment, survival analysis, clustering,
+CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric
+manner.")
+ (license license:gpl2+)))
+
(define-public r-harshlight
(package
(name "r-harshlight")
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