scanpy.tl.score_genes_cell_cycle

scanpy.tl.score_genes_cell_cycle(adata, s_genes, g2m_genes, copy=False, **kwargs)

Score cell cycle genes [Satija15].

Given two lists of genes associated to S phase and G2M phase, calculates scores and assigns a cell cycle phase (G1, S or G2M). See score_genes() for more explanation.

Parameters

adata : AnnData: The annotated data matrix.
s_genes : Sequence[str]: List of genes associated with S phase.
g2m_genes : Sequence[str]: List of genes associated with G2M phase.
copy : bool (default: False): Copy adata or modify it inplace.
**kwargs: Are passed to score_genes(). ctrl_size is not possible, as it’s set as min(len(s_genes), len(g2m_genes)).

Return type

Optional[AnnData]

Returns

Depending on copy, returns or updates adata with the following fields.

S_scoreadata.obs, dtype object: The score for S phase for each cell.
G2M_scoreadata.obs, dtype object: The score for G2M phase for each cell.
phaseadata.obs, dtype object: The cell cycle phase (S, G2M or G1) for each cell.