Package: liger
Type: Package
Title: Lightweight Iterative Geneset Enrichment
Version: 2.0.1
Authors@R: c(person("Jean", "Fan", role = c("aut", "cre"), email = "jeanfan@jhu.edu", comment = c(ORCID = "0000-0002-0212-5451")), person("Peter", "Kharchenko", role = "aut", email = "Peter_Kharchenko@hms.harvard.edu"))
Description: 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.
License: GPL-3 | file LICENSE
LazyData: TRUE
Depends: R (>= 2.10)
Imports: graphics, stats, Rcpp, matrixStats, parallel
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
URL: https://github.com/JEFworks/liger
BugReports: https://github.com/JEFworks/liger/issues
RoxygenNote: 7.1.0
Author: Jean Fan [aut, cre] (<https://orcid.org/0000-0002-0212-5451>),
  Peter Kharchenko [aut]
NeedsCompilation: yes
Packaged: 2021-01-25 01:25:15 UTC; Jean
Maintainer: Jean Fan <jeanfan@jhu.edu>
Repository: CRAN
Date/Publication: 2021-01-25 05:50:09 UTC
Built: R 4.2.3; x86_64-w64-mingw32; 2024-04-24 01:15:26 UTC; windows
ExperimentalWindowsRuntime: ucrt
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