scvelo.tl.score_genes_cell_cycle
- scvelo.tl.score_genes_cell_cycle(adata, s_genes=None, g2m_genes=None, copy=False, **kwargs)
Score cell cycle genes.
Calculates scores and assigns a cell cycle phase (G1, S, G2M) using the list of cell cycle genes defined in [Tirosh et al., 2016].
- Parameters:
adata – The annotated data matrix.
s_genes – List of genes associated with S phase.
g2m_genes – List of genes associated with G2M phase.
copy – 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)).
- Returns:
S_score (adata.obs, dtype object) – The score for S phase for each cell.
G2M_score (adata.obs, dtype object) – The score for G2M phase for each cell.
phase (adata.obs, dtype object) – The cell cycle phase (S, G2M or G1) for each cell.