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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: 4.0.5
Depends: R (≥ 3.5.0)
Imports: AnnotationDbi, corpcor, data.table, dplyr, genefilter, graph, graphite, glmnet, glassoFast, httr, igraph, magrittr, Matrix, msigdbr, org.Hs.eg.db, quadprog, RCy3, reshape2, rlang, Rcpp (≥ 1.0.2)
LinkingTo: Rcpp, RcppEigen
Suggests: knitr, MASS, rmarkdown
Published: 2023-11-14
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.pdf
Vignettes: Introduction to netgsa

Downloads:

Package source: netgsa_4.0.5.tar.gz
Windows binaries: r-devel: netgsa_4.0.5.zip, r-release: netgsa_4.0.5.zip, r-oldrel: netgsa_4.0.5.zip
macOS binaries: r-release (arm64): netgsa_4.0.5.tgz, r-oldrel (arm64): netgsa_4.0.5.tgz, r-release (x86_64): netgsa_4.0.5.tgz, r-oldrel (x86_64): netgsa_4.0.5.tgz
Old sources: netgsa archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=netgsa to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.