Gene Set Enrichment Analysis in R

R-interface to C++ implementation of the rank/score permutation based GSEA test (Subramanian et al 2005 ).


gsEasy 1.3

  • Fixed bug, now ensuring absolute value of correlation parameter r is used to compute enrichment score (credit to Michael from Berkeley).

gsEasy 1.1

  • Now includes GO term gene sets data object (i.e. a list of character vectors, named by GO term, of genes associated with each term - can be loaded with data(GO_gene_sets) [based on Gene Ontology (2015-11-27) and human GO annotations file validated on 07/08/2016]).
  • Change in how S argument of gset is interpreted when vector of scores r is supplied - now instead of the scores for S being those at the corresponding ranks in r, they are those at corresponding indices. For example, in version 1.0 the scores for S=1:3 would be the top 3 scores in r, however now it be the those of the first 3 elements of r. Behaviour has not changed for when S is character or when N is used instead of r.

Reference manual

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1.3 by Daniel Greene, 8 months ago

Browse source code at

Authors: Daniel Greene

Documentation:   PDF Manual  

GPL (>= 2) license

Imports Rcpp, ontologyIndex

Suggests knitr

Linking to Rcpp

See at CRAN