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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 [issues need fixing before 2024-08-18] |
Reference manual: | netgsa.pdf |
Vignettes: |
Introduction to netgsa |
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 |
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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.
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