scatrans.run_kegg

scatrans.run_kegg(gene_list, organism='mouse', universe=None, background=None, adata=None, pval_cutoff=None, padj_cutoff=None, min_size=5, max_size=500, restrict_background_to_gene_sets=True, force_universe=False, return_all=False, verbose=True, gene_case=None, kegg_library=None, gene_set_source='scatrans', include_gene_list=False, **kwargs)

KEGG pathway enrichment (wrapper around run_enrichment).

Defaults to the bundled scATrans (clusterProfiler-derived) gene set. You only need to specify the organism.

To use a specific original Enrichr version, just pass the full name:

kegg_library=”KEGG_2021” # or KEGG_2019, KEGG_2016, etc.

gene_set_source can be used as an explicit override (“scatrans” or “enrichr”) if needed.

Supports the same universe/background controls as run_enrichment for clusterProfiler-like conservative behavior by default.

Note: internal organism is normalized to lowercase (e.g. “mouse”) for attrs.

Parameters:

• gene_list (Iterable[Any])

• organism (str)

• universe (Iterable[Any] | None)

• background (Iterable[Any] | None)

• adata (Any | None)

• pval_cutoff (float | None)

• padj_cutoff (float | None)

• min_size (int)

• max_size (int)

• restrict_background_to_gene_sets (bool)

• force_universe (bool)

• return_all (bool)

• verbose (bool)

• gene_case (str | None)

• kegg_library (str | None)

• gene_set_source (str)

• include_gene_list (bool)

• kwargs (Any)

Return type:

DataFrame