, *, s_genes, g2m_genes, copy=False, **kwargs)[source]#

Score cell cycle genes [Satija et al., 2015].

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.

adata AnnData

The annotated data matrix.

s_genes Sequence[str]

List of genes associated with S phase.

g2m_genes Sequence[str]

List of genes associated with G2M phase.

copy bool (default: False)

Copy adata or modify it inplace.


Are passed to score_genes(). ctrl_size is not possible, as it’s set as min(len(s_genes), len(g2m_genes)).

Return type:

AnnData | None


Returns None if copy=False, else returns an AnnData object. Sets the following fields:

adata.obs['S_score']pandas.Series (dtype object)

The score for S phase for each cell.

adata.obs['G2M_score']pandas.Series (dtype object)

The score for G2M phase for each cell.

adata.obs['phase']pandas.Series (dtype object)

The cell cycle phase (S, G2M or G1) for each cell.

See also



See this notebook.