ILRI Research Computing

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====== Gene Set Enrichment Analysis(GSEA) ======

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). 

===== Information =====

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

===== Usage =====

See which versions of GSEA are available:
<code>$ module avail gsea</code>

Load gsea
<code>$ module load gsea/2.2.3</code>

===== Installation ======

Notes from the sysadmin during installation:
<code>
$ 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/
</code>

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<code>#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/gsea2-2.2.3.jar $*
</code>