omicverse.pp.score_genes_cell_cycle¶

omicverse.pp.score_genes_cell_cycle(adata, species='human', s_genes=None, g2m_genes=None)[source]¶

Score cell cycle phases using predefined or custom gene sets.

Parameters:

adata – Annotated data matrix with rows for cells and columns for genes.
species (default: 'human') – The species of the data (‘human’ or ‘mouse’). Default: ‘human’.
s_genes (default: None) – Custom list of S phase genes. Default: None (uses predefined).
g2m_genes (default: None) – Custom list of G2M phase genes. Default: None (uses predefined).

Returns:

Updates adata.obs with ‘S_score’, ‘G2M_score’, and ‘phase’ columns.

Return type:

None

Examples

>>> import omicverse as ov
>>> # Score cell cycle for human data
>>> ov.pp.score_genes_cell_cycle(adata, species='human')
>>> # Check results
>>> print(adata.obs[['S_score', 'G2M_score', 'phase']].head())