liger: Lightweight Iterative Geneset Enrichment

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: 0.1
Depends: R (≥ 2.10)
Imports: graphics, stats, Rcpp, matrixStats, parallel
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown
Published: 2018-06-14
Author: Jean Fan ORCID iD [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

Downloads:

Reference manual: liger.pdf
Vignettes: Vignette Title
Vignette Title
Package source: liger_0.1.tar.gz
Windows binaries: r-devel: liger_0.1.zip, r-release: liger_0.1.zip, r-oldrel: liger_0.1.zip
OS X binaries: r-release: liger_0.1.tgz, r-oldrel: liger_0.1.tgz

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