GSEA exercises as part of the Transcriptomics Module (2023-2024).

Conda environment installation (for exercises in R)

1. Clone this repository:

git clone https://github.com/bioinfo-lessons/gsea

2. Go to gsea folder:

cd gsea/

3. Install a new conda environment using the provided YAML:

mamba env create -f envs/gsea.yaml

4. Activate the environment:

conda activate ISCIII_GSEA

5. Deactivate when finished:

conda deactivate

GSEA installation (Linux)

1. Go to GSEA official webpage. Click on download GSEA_Linux_4.3.3.zip.

2. Save GSEA folder whenever you want (e.g. your home directory: ~/).

3. Uncompress the zip.

GSEA server launch

1. Go to GSEA folder:

cd ~/GSEA_Linux_4.3.3/

2. Run the following command (java >= 11 required):

java --module-path=modules -Xmx4g @gsea.args --patch-module=jide.common=lib/jide-components-3.7.4.jar:lib/jide-dock-3.7.4.jar:lib/jide-grids-3.7.4.jar --module=org.gsea_msigdb.gsea/xapps.gsea.GSEA