scanpy.tl.score_genes_cell_cycle#
- scanpy.tl.score_genes_cell_cycle(adata, *, 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.- Parameters:
- 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.- **kwargs
Are passed to
score_genes()
.ctrl_size
is not possible, as it’s set asmin(len(s_genes), len(g2m_genes))
.
- adata
- Return type:
- Returns:
Returns
None
ifcopy=False
, else returns anAnnData
object. Sets the following fields:adata.obs['S_score']
pandas.Series
(dtypeobject
)The score for S phase for each cell.
adata.obs['G2M_score']
pandas.Series
(dtypeobject
)The score for G2M phase for each cell.
adata.obs['phase']
pandas.Series
(dtypeobject
)The cell cycle phase (
S
,G2M
orG1
) for each cell.
See also
Examples
See this notebook.