scib.preprocessing.score_cell_cycle

scib.preprocessing.score_cell_cycle(adata: AnnData, organism: Literal['mouse', 'mus musculus', 'mus_musculus', 'human', 'homo sapiens', 'homo_sapiens', 'c_elegans', 'c elegans', 'caenorhabditis elegans', 'caenorhabditis_elegans', 'zebrafish', 'danio rerio', 'danio_rerio'] = 'mouse')

Score cell cycle score given an organism

Wrapper function for scanpy.tl.score_genes_cell_cycle

Tirosh et al. cell cycle marker genes downloaded from https://raw.githubusercontent.com/theislab/scanpy_usage/master/180209_cell_cycle/data/regev_lab_cell_cycle_genes.txt

See more on gene sets in get_cell_cycle_genes().

This function picks gene IDs or gene names of the cell cycle genes, depending on what is present in the adata object.

Parameters:

• adata – anndata object containing

• organism – organism of gene names to match cell cycle genes

Returns:

tuple of (s_genes, g2m_genes) of S-phase genes and G2- and M-phase genes scores