tools.exportDEres

tools.exportDEres(adata, column=None, filename=None, remove_mito_ribo=True, key='rank_genes_groups')[source]

Export DE results from scanpy.

Parameters:

  • adata (AnnData) – AnnData object with sc.tl.rank_genes_groups performed.

  • column (Optional[str], optional) – specific contrast to return.

  • filename (Optional[str], optional) – if provided, save as file. Otherwise, return as DataFrame.

  • remove_mito_ribo (bool, optional) – whether to filter all mito and ribo genes in the output.

  • key (str, optional) – name in .uns to retrieve DE results.

Returns:

DataFrame of DE results.

Return type:

DataFrame