bioalpha.singlecell.read_gene_signatures_GSEA

bioalpha.singlecell.read_gene_signatures_GSEA(name: str, organism: Literal['Human', 'Mouse', 'Yeast', 'Fly', 'Fish', 'Worm'] = 'Human', adata: AnnData | None = None, key_added: str | None = None, copy: bool = False, **kwargs) → List[GeneSignature] | AnnData | None

Read gene signatures from GSEA (https://www.gsea-msigdb.org/).

Parameters:

  • name (str) – A gene_sets.gmt file or an enrichr library name.

  • organism (str, default = 'Human') – One from {'Human', 'Mouse', 'Yeast', 'Fly', 'Fish', 'Worm'}. This arugment has not effect if input is a .gmt file.

  • adata (Optional[AnnData], default = None) – The annotated data matrix of shape n_obs x n_vars. If passed a not None value, gene_signatures will be saved in adata.uns. Otherwise, return a list gene signatures.

  • key_added (Optional[str], default = None) – The key in adata.uns information is saved to. Can not be set when adata is None.

  • copy (bool, default = False) – Whether to copy adata or modify it inplace.

Returns:

  • If adata is passed, "gene_sigs" will be added in

  • adata.uns and returned if copy = True.

  • Otherwise, return a List[GeneSignature].