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: |
4.0.6 |
| 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: |
2025-07-30 |
| 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:
Downloads:
Linking:
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