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:

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