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 : list

List of genes associated with S phase.

g2m_genes : list

List of genes associated with G2M phase.

copy : bool, optional (default: False)

Copy adata or modify it inplace.

**kwargs : optional keyword arguments

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.

See also

score_genes()

Examples

See this notebook.