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, 2015 (https://doi.org/10.1126/science.aad0501).
- 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.