netgsa: Network-Based Gene Set Analysis

Carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. 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>.

Version:	4.0.7
Depends:	R (≥ 3.5.0)
Imports:	AnnotationDbi, corpcor, data.table, dplyr, genefilter, graph, graphite, glmnet, glassoFast, httr, igraph, magrittr, Matrix, msigdbr, quadprog, RCy3, reshape2, rlang, Rcpp (≥ 1.0.2)
LinkingTo:	Rcpp, RcppEigen
Suggests:	knitr, MASS, org.Hs.eg.db, rmarkdown
Published:	2026-01-16
DOI:	10.32614/CRAN.package.netgsa
Author:	Michael Hellstern [aut, cre], Ali Shojaie [aut], Jing Ma [aut], Kun Yue [aut]
Maintainer:	Michael Hellstern <mikeh1 at uw.edu>
License:	GPL (≥ 3)
URL:	https://github.com/mikehellstern/netgsa
NeedsCompilation:	yes
Materials:	README, NEWS
In views:	Omics
CRAN checks:	netgsa results

Documentation:

Reference manual:	netgsa.html , netgsa.pdf
Vignettes:	Introduction to netgsa (source, R code)

Downloads:

Package source:	netgsa_4.0.7.tar.gz
Windows binaries:	r-devel: netgsa_4.0.7.zip, r-release: netgsa_4.0.7.zip, r-oldrel: netgsa_4.0.7.zip
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): netgsa_4.0.6.tgz, r-release (x86_64): netgsa_4.0.7.tgz, r-oldrel (x86_64): netgsa_4.0.7.tgz
Old sources:	netgsa archive

Reverse dependencies:

Reverse imports:

DNEA

Linking:

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