scanpy_plus.pp.cellcycle_corr module

scanpy_plus.pp.cellcycle_corr.cellcycle_corr(data, cell_cycle_genes=None, sim_cutoff=0.2)

Finds genes highly correlated with cell cycle genes.

data: anndata. X MUST be LOGNORM cell_cycle_genes: list of cell cycle genes(1) sim_cutoff: Similarity cutoff

returns: list(list) gene_correlation = matrix

genes_to_retain = genes to retain

1. cell_cycle_genes = [x.strip().capitalize() for x in open(‘public_data/regev_lab_cell_cycle_genes.txt’)] For human. no need to capitalize()