omicverse.single.pathway_aucell

omicverse.single.pathway_aucell(adata, pathway_names, pathways_dict, AUC_threshold=0.01, seed=42)[source]

Calculate the area under the curve (AUC) for a set of pathways in an AnnData object.

Parameters:

  • adata (anndata.AnnData) – AnnData containing expression matrix.

  • pathway_names (list) – Ordered pathway names to score.

  • pathways_dict (dict) – Mapping from pathway name to list of genes.

  • AUC_threshold (float) – AUCell rank threshold percentile.

  • seed (int) – Random seed for ranking backend.

Returns:

Writes per-pathway AUCell scores to adata.obs.

Return type:

None