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: | 4.0.0 |
| 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: | 2021-05-15 |
| 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 |
| CRAN checks: | netgsa results |
| Reference manual: | netgsa.pdf |
| Vignettes: |
Introduction to netgsa |
| Package source: | netgsa_4.0.0.tar.gz |
| Windows binaries: | r-devel: netgsa_4.0.0.zip, r-devel-UCRT: netgsa_4.0.0.zip, r-release: netgsa_4.0.0.zip, r-oldrel: netgsa_4.0.0.zip |
| macOS binaries: | r-release (arm64): not available, r-release (x86_64): netgsa_3.1.0.tgz, r-oldrel: netgsa_3.1.0.tgz |
| Old sources: | netgsa archive |
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