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authorRicardo Wurmus <rekado@elephly.net>2024-01-21 08:33:56 +0100
committerRicardo Wurmus <rekado@elephly.net>2024-01-21 08:33:56 +0100
commit0facea431a83dd3495a2f35aa1081cb186cdcd99 (patch)
tree0f13257dca4d8cff15d8524c391021b90d29e30c /gnu/packages
parent815e378deef8a2ca088cd6a13578ce81b331a05c (diff)
downloadguix-0facea431a83dd3495a2f35aa1081cb186cdcd99.tar.gz
guix-0facea431a83dd3495a2f35aa1081cb186cdcd99.zip
gnu: Add r-netgsa.
* gnu/packages/bioconductor.scm (r-netgsa): New variable. Change-Id: I79b842854db80bbacdb8ff4c9fccfabdfc04d779
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioconductor.scm46
1 files changed, 46 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4b2fe75994..f3419900f5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6188,6 +6188,52 @@ multiple features (e.g. genes). @code{Seurat} and @code{SingleCellExperiment}
objects can be used within Nebulosa.")
(license license:gpl3)))
+;; This is a CRAN package but it requires r-rcy3, a Bioconductor package.
+(define-public r-netgsa
+ (package
+ (name "r-netgsa")
+ (version "4.0.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "netgsa" version))
+ (sha256
+ (base32 "1m9myxsbvbljr038azxzakpbh20a21qhiy20d0ipvjc5asq3kfla"))))
+ (properties `((upstream-name . "netgsa")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-annotationdbi
+ r-corpcor
+ r-data-table
+ r-dplyr
+ r-genefilter
+ r-glassofast
+ r-glmnet
+ r-graph
+ r-graphite
+ r-httr
+ r-igraph
+ r-magrittr
+ r-matrix
+ r-msigdbr
+ r-org-hs-eg-db
+ r-quadprog
+ r-rcpp
+ r-rcppeigen
+ r-rcy3
+ r-reshape2
+ r-rlang))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/mikehellstern/netgsa")
+ (synopsis "Network-Based gene set analysis")
+ (description
+ "This package lets you carry out network-based gene set analysis by
+incorporating external information about interactions among genes, as well as
+novel interactions learned from data. It implements methods described in
+Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A,
+Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A,
+Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.")
+ (license license:gpl3+)))
+
;; This is a CRAN package, but it depends on Bioconductor packages.
(define-public r-nmf
(package