skills/pathway-enrichment/scripts/run_enrichment.py

• _clean_symbols · function · L52-L66 — def _clean_symbols(genes, organism: str)
• _read_gene_list · function · L69-L75 — def _read_gene_list(path: Path)
• _build_rank_from_deseq2 · function · L78-L98 — def _build_rank_from_deseq2(path: Path, organism: str) -> pd.Series
• _read_rnk · function · L101-L115 — def _read_rnk(path: Path, organism: str) -> pd.Series
• _clean_index · function · L118-L124 — def _clean_index(index, organism: str)
• _dotplot · function · L127-L134 — def _dotplot(df: pd.DataFrame, column: str, title: str, outpath: Path)
• run_ora · function · L137-L155 — def run_ora(args)
• run_gsea · function · L158-L182 — def run_gsea(args)
• main · function · L185-L227 — def main()