dynamo.pp.cell_cycle_scores(adata, layer=None, gene_list=None, refine=True, threshold=0.3, copy=False)[source]

Estimate cell cycle stage of each cell based on its gene expression pattern.

If more direct control is desired, use get_cell_phase.

  • adata (AnnData) – an anndata object.

  • layer (Optional[str]) – The layer of data to use for calculating correlation. If None, use adata.X. Defaults to None.

  • gene_list (Optional[OrderedDict]) – OrderedDict of marker genes to use for cell cycle phases. If None, the default list will be used. Defaults to None.

  • refine (bool) – whether to refine the gene lists based on how consistent the expression is among the groups. Defaults to True.

  • threshold (float) – threshold on correlation coefficient used to discard genes (expression of each gene is compared to the bulk expression of the group and any gene with a correlation coefficient less than this is discarded). Defaults to 0.3.

  • copy (bool) – whether copy the original AnnData object and return it. Defaults to False.

Return type:



Returns an updated adata object with cell_cycle_phase as new column in .obs and a new data frame with cell_cycle_scores key to .obsm where the cell cycle scores indicating the likelihood a given cell is in a given cell cycle phase if copy is true. Otherwise, return None.