omicverse.bulk.geneset_enrichment

omicverse.bulk.geneset_enrichment#

omicverse.bulk.geneset_enrichment(gene_list, pathways_dict, pvalue_threshold=0.05, pvalue_type='auto', organism='Human', description='None', background=None, outdir='./enrichr', cutoff=0.5)[source]#

Perform pathway enrichment analysis using Enrichr-compatible gene-set libraries.

Parameters:

  • gene_list (list) – Input gene symbols (typically DEGs) for enrichment testing.

  • pathways_dict (dict|str) – Gene sets — a prepared dict (ov.utils.geneset_prepare), a .gmt/.txt path, or an Enrichr library name (resolved and auto-downloaded internally).

  • pvalue_threshold (float, optional) – Significance threshold used to filter enrichment terms.

  • pvalue_type (str, optional) – P-value mode: auto/adjust/raw P-value filtering.

  • organism (str, optional) – Organism label passed to Enrichr backend (for example Human/Mouse).

  • description (str, optional) – Job description tag stored in output metadata.

  • background (list|None, optional) – Optional background gene universe. If None, species defaults are used.

  • outdir (str, optional) – Directory for enrichment output files.

  • cutoff (float, optional) – Enrichr internal cutoff threshold.

Returns:

Enrichment result table with statistics and derived plotting columns.

Return type:

pandas.DataFrame

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