omicverse.bulk.pyGSEA

omicverse.bulk.pyGSEA(gene_rnk: DataFrame, pathways_dict: dict, processes: int = 8, permutation_num: int = 100, outdir: str = './enrichr_gsea', cutoff: float = 0.5) → None[source]

Gene Set Enrichment Analysis (GSEA) wrapper for ranked gene lists.

Parameters:

  • gene_rnk (pd.DataFrame) – Ranked gene table used for enrichment scoring.

  • pathways_dict (dict) – Mapping from pathway name to gene-set members.

  • processes (int, optional, default=8) – Number of worker processes.

  • permutation_num (int, optional, default=100) – Number of permutations for enrichment significance.

  • outdir (str, optional, default='./enrichr_gsea') – Output directory for reports and plots.

  • cutoff (float, optional, default=0.5) – Significance/score threshold for result filtering.

Returns:

Initializes GSEA analysis settings.

Return type:

None

Examples

>>> # Initialize GSEA object