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.