[aut, cre],
Peter Kharchenko [aut]Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. The original algorithm is detailed in Subramanian et al. with 'Java' implementations available through the Broad Institute (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>). The 'liger' package provides a lightweight R implementation of this enrichment test on a list of values (Fan et al., 2017 <doi:10.5281/zenodo.887386>). Given a list of values, such as p-values or log-fold changes derived from differential expression analysis or other analyses comparing biological states, this package enables you to test a priori defined set of genes for enrichment to enable interpretability of highly significant or high fold-change genes.
| Version: | 1.0 |
| Depends: | R (≥ 2.10) |
| Imports: | graphics, stats, Rcpp, matrixStats, parallel |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | knitr, rmarkdown |
| Published: | 2019-01-03 |
| Author: | Jean Fan [aut, cre],
Peter Kharchenko [aut] |
| Maintainer: | Jean Fan <jeanfan at fas.harvard.edu> |
| BugReports: | https://github.com/JEFworks/liger/issues |
| License: | GPL-3 | file LICENSE |
| URL: | https://github.com/JEFworks/liger |
| NeedsCompilation: | yes |
| Materials: | README NEWS |
| CRAN checks: | liger results |
| Reference manual: | liger.pdf |
| Vignettes: |
Gene Set Enrichment Analysis with LIGER Interpreting LIGER results Highlighting the Power of Gene Set Enrichment Analysis using Simulation |
| Package source: | liger_1.0.tar.gz |
| Windows binaries: | r-devel: liger_1.0.zip, r-release: liger_1.0.zip, r-oldrel: liger_1.0.zip |
| OS X binaries: | r-release: liger_1.0.tgz, r-oldrel: liger_0.1.tgz |
| Old sources: | liger archive |
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