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(e.g. phenotypes).

• Version: 2.2.3
• Added: February, 2017
• Link: http://software.broadinstitute.org/gsea/index.jsp

See which versions of GSEA are available:

$ module avail gsea

Load gsea

$ module load gsea/2.2.3

Notes from the sysadmin during installation:

$ cd /tmp
$ wget "http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/software/gsea2-2.2.3.jar" -O gsea2-2.2.3.jar
$ sudo mkdir -p /export/apps/gsea/2.2.3/
$ sudo cp gsea2-2.2.3.jar /export/apps/gsea/2.2.3/

I created a generic gsea wrapper shell script for running gsea2-2.2.3.jar, as it must otherwise be run with java -jar .. which is rather user-unfriendly.

/export/apps/gsea/2.2.3/gsea2-2.2.3.jar

#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/gsea2-2.2.3.jar $*