funkea: Functional Enrichment Analysis in Python

Benjamin Tenmann, Karina Close, Andrea Rodriguez-Martinez, Sam Abujudeh

Abstract: Advancements in Genome-wide association studies (GWAS) have led to the discovery of numerous genetic variants potentially linked to various traits, necessitating effective methods to interpret and summarise these vast data sets. We introduce funkea, a Python package designed to fill this need by providing functional enrichment analysis methods. This tool encompasses popular enrichment approaches under a unified interface and leverages Spark for virtually limitless scale. This allows researchers to conduct pathway, cell-type, and tissue enrichment analysis across diverse annotation datasets. Ultimately, the funkea Python package delivers a highly flexible and scalable solution for functional enrichment analysis in the context of modern genetics workflows. https://github.com/BenevolentAI/funkea