sccloud.markers

sccloud.markers(data, head=None, de_key='de_res', sort_by='auroc, WAD_score', alpha=0.05)[source]
Parameters

  • data (anndata.AnnData) – Annotated data matrix with rows for cells and columns for genes.

  • head (int, optional, default: None) – List only top head genes for each cluster. If None, show any DE genes.

  • de_key (str, optional, default, de_res) – Keyword of DE result stored in data.varm.

  • sort_by (str, optional, default: "auroc,WAD_score") – Sort the resulting marker dictionary by auroc and WAD_score.

  • alpha (float, optional, default: 0.05) – q-value threshold for getting valid DE genes. Only those with q-value of any test below alpha are significant, and thus considered as DE genes.

Returns

results – A Python dictionary containing markers in structure dict[cluster_id]['up' or 'down'][dataframe].

Return type

Dict[str, Dict[str, pd.DataFrame]]

Examples

>>> marker_dict = scc.markers(adata)