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) – Gene-set dictionary loaded by
ov.utils.geneset_prepare.pvalue_threshold (float, optional) – Significance threshold used to filter enrichment terms.
pvalue_type (str, optional) – P-value mode:
auto/adjust/rawP-valuefiltering.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: