This repository contains a script [gsea.py], that runs a geneset enrichment analysis for genesets described in terms of M. tuberculosis H37Rv locus tags. It uses the COMBAT TB NeoDb.
Requirements:
click
statsmodels
scipy
neo4j_python_driverand Python > 3.6. To install these requirements with conda, run conda create --name gsea --file environment.txt where
gsea is the name of the conda environment you are creating (you can change it if you like). Then activate the environment with conda activate gsea before running the gsea.py script.