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: 4.0.1
Depends: R (≥ 3.5.0)
Imports: AnnotationDbi, corpcor, data.table, dplyr, genefilter, graph, graphite, glmnet, glassoFast, httr, igraph, jsonlite, magrittr, Matrix, msigdbr, ndexr, org.Hs.eg.db, quadprog, RCy3, reshape2, rlang, Rcpp (≥ 1.0.2)
LinkingTo: Rcpp, RcppEigen
Suggests: knitr, MASS, rmarkdown
Published: 2021-09-13
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
CRAN checks: netgsa results

Downloads:

Reference manual: netgsa.pdf
Vignettes: Introduction to netgsa
Package source: netgsa_4.0.1.tar.gz
Windows binaries: r-devel: netgsa_4.0.1.zip, r-devel-UCRT: netgsa_4.0.1.zip, r-release: netgsa_4.0.0.zip, r-oldrel: netgsa_4.0.1.zip
macOS binaries: r-release (arm64): netgsa_4.0.0.tgz, r-release (x86_64): netgsa_3.1.0.tgz, r-oldrel: netgsa_3.1.0.tgz
Old sources: netgsa archive

Linking:

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