stat tests

Compute ranking of differential genes between groups using statistical tests such as t-test.

Parameters

method: str Statistical test to find differential clusters and results in adata for plotting. Options include t-test, t-test_overestim_var, wilcoxon and logreg.

group_by: str Obs value to group clusters by.

Web view

Python equivalent

import scanpy as sc

sc.tl.rank_genes_groups(adata, groupby=group_by, method = "wilcoxon")
sc.pl.rank_genes_groups(adata, n_genes=25, sharey=False, save=True)