Dual Python and R notebook that compares ouput for two methods of Gene Set Enrichment Analysis (GSEA) of GSEApy and fGSEA. GSEApy is the Python/Rust implementation of GSEA and contains the prerank version and traditional version of GSEA whilst fGSEA is the R package for Fast GSEA. This notebook allows users to explore the differences in GSEA results when employing different settings(e.g: ranking metric, gene sets, permutation type, threads, minimum and maximum size of genes).
- Install Python and R
- Install Rpy2 by running the following command in Bash:
pip install rpy2
- Download the Jupyter Notebook (.ipynb) and example input files:'GSEApy-fGSEA-exampleinputfiles' from the gh-pages branch.
- Open the Jupyternotebook in Jupyterlab or Jupyternotebook.
- Run the cells of the notebook document step-by-step (one cell a time) by pressing shift + enter or run the whole notebook in a single step by clicking on the menu Cell -> Run All.
- Adapt the notebook with your own dataset and/or parameters of interest to compare your GSEA findings.