scib.preprocessing.score_cell_cycle

scib.preprocessing.score_cell_cycle(adata, organism='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

For human, mouse genes are capitalised and used directly. This is under the assumption that cell cycle genes are well conserved across species.

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