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: 2.0.1
Depends: R (≥ 2.10)
Imports: graphics, stats, Rcpp, matrixStats, parallel
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, testthat
Published: 2021-01-25
Author: Jean Fan ORCID iD [aut, cre], Peter Kharchenko [aut]
Maintainer: Jean Fan <jeanfan at>
License: GPL-3 | file LICENSE
NeedsCompilation: yes
Citation: liger citation info
Materials: README NEWS
In views: Omics
CRAN checks: liger results [issues need fixing before 2024-06-14]


Reference manual: liger.pdf
Vignettes: Gene Set Enrichment Analysis with LIGER
Interpreting liger results
Exploring Permutation P-values
Highlighting the Power of Gene Set Enrichment Analysis using Simulation


Package source: liger_2.0.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): liger_2.0.1.tgz, r-oldrel (arm64): liger_2.0.1.tgz, r-release (x86_64): liger_2.0.1.tgz, r-oldrel (x86_64): liger_2.0.1.tgz
Old sources: liger archive

Reverse dependencies:

Reverse imports: STdeconvolve


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