omicverse.single.get_celltype_marker

omicverse.single.get_celltype_marker(adata, clustertype='leiden', log2fc_min=2, scores_type='scores', pval_cutoff=0.05, rank=True, key='rank_genes_groups', method='wilcoxon', foldchange=None, topgenenumber=10, unique=True, global_unique=False, use_raw=None, layer=None, **kwargs)[source]

Get marker genes for each cluster/cell type.

Parameters:

  • adata (anndata.AnnData) – AnnData containing cluster annotations and expression matrix.

  • clustertype (str) – Column in adata.obs used to define groups.

  • log2fc_min (int) – Minimum log2 fold-change threshold when extracting DE markers.

  • scores_type (str) – Statistic field used for thresholding (for example 'scores').

  • pval_cutoff (float) – Maximum adjusted p-value cutoff for retained markers.

  • rank (bool) – Whether to run sc.tl.rank_genes_groups before extraction.

  • key (str) – Key in adata.uns storing ranked-gene results.

  • method (str) – Differential-expression method for rank_genes_groups.

  • foldchange (float or None) – Optional manual score threshold; auto-derived when None.

  • topgenenumber (int) – Maximum number of markers retained per cluster.

  • unique (bool) – Whether to deduplicate markers within each cluster.

  • global_unique (bool) – Whether to enforce uniqueness across all clusters.

  • use_raw (Optional[bool]) – Forwarded to rank_genes_groups to control raw usage.

  • layer (Optional[str]) – Layer passed to rank_genes_groups.

  • **kwargs – Additional keyword arguments for rank_genes_groups.

Returns:

Dictionary mapping cluster labels to marker gene lists.

Return type:

dict