gsea-enrichment-analysis

Gene set enrichment analysis fails with file paths because the API requires a dictionary object. You must load your gene sets using geneset_prepare() to convert pathway files into a compatible dictionary before running the enrichment function.

To run GSEA on mouse DEG datasets, load your DEG results, install the pathway database, prepare gene sets with geneset_prepare(), and execute geneset_enrichment(). The workflow supports both human and mouse organisms for end-to-end pathway analysis.

Supported gene set file formats include .txt, .gmt, and .json. These formats allow broad compatibility with common pathway databases when loading and preparing your gene sets for enrichment analysis.

This GSEA workflow requires basic familiarity with bioinformatics concepts like DEGs and pathway databases. You need to understand how to load data, call preparation functions, and execute the enrichment API within your programming environment.

The best way to prepare downloaded pathway databases is using the geneset_prepare() utility. It correctly parses your downloaded database files and transforms them into the dictionary format required by the geneset_enrichment() function.