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README.md

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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
  1. Go to gsea folder:
cd gsea/
  1. Install a new conda environment using the provided YAML:
mamba env create -f envs/gsea.yaml
  1. Activate the environment:
conda activate ISCIII_GSEA
  1. 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/
  1. 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