voyagerpy.utils.get_marker_genes#

voyagerpy.utils.get_marker_genes(adata: AnnData, hvg: bool = False, hvg_string: str = 'highly_variable', cluster: str = 'cluster') → DataFrame#

Find marker genes for each cluster.

Similar to find_markers but returns only, top marker genes for each cluster, with no additional information.

Parameters:

  • adata (AnnData) – AnnData object with defined clustering in adata.obs.

  • hvg (bool, optional) – Whether to only test highly variable genes. The default is False.

  • hvg_string (str, optional) – String to identify highly variable genes in adata.var. The default is “highly_variable”.

  • cluster (str, optional) – String to identify cluster column in adata.obs. The default is “cluster”.

Returns:

DataFrame with each column corresponding to differentially expressed genes for each cluster in descending order.

Return type:

DataFrame