scib.preprocessing.get_cell_cycle_genes

scib.preprocessing.get_cell_cycle_genes(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'])

Get cell cycle genes for a given organism

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

For organisms other than human or mouse, orthlogy-mapped datasets from Tinyaltas were used: https://github.com/hbc/tinyatlas/tree/master/cell_cycle

Parameters:

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

• identifier – gene identifier to use. options: “gene_name”, “gene_id”