GSEAlite

This is my implementation of the Gene Set Enrichment Analysis methodology (http://www.broadinstitute.org/gsea/index.jsp; Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) and Mootha, Lindgren, et al. (2003, Nat Genet 34, 267-273)).

The package gives access to the typical plot function: Enrichment Analysis and to the analysis of list of gene sets. p-values, FDR, ES and NES are computed.

A read.gmt function allows to load gene set collection from MSigDB (http://www.broadinstitute.org/gsea/msigdb/index.jsp)

Input parameters allow users to define their own metric function. The two default metric functions are signal-to-noise and fold changes.