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

Call cell cycle positions for cells within the population. If more direct control is desired, use get_cell_phase.

  • adata (an anndata object.) –

  • layer (str or None (default: None)) – The layer of data to use for calculating correlation. If None, use adata.X.

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

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

  • threshold (float or None (default: 0.3)) – 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)

  • copy (bool) – If true, copy the original AnnData object and return it

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.