omicverse.bulk.pyGSEA

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omicverse.bulk.pyGSEA#

omicverse.bulk.pyGSEA(gene_rnk: DataFrame, pathways_dict: dict, processes: int = 1, permutation_num: int = 1000, outdir: str = './enrichr_gsea', cutoff: float = 0.5, organism: str = 'Human', backend: str = 'numpy', weight: float = 1.0, min_size: int = 15, max_size: int = 500, progress: bool = True) → 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|str) – Gene sets — a prepared dict, a .gmt/.txt path, or an Enrichr library name (resolved and auto-downloaded internally).

  • 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
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