chansigit / scanpy_deg

enhanced DEG analysis in scanpy

scanpy_deg

enhanced DEG analysis in scanpy

usage

perform group1-vs-group2 analysis

deg_by_cell_lists(adata, 
                  index_list1=cell_indices_1, index_list2=cell_indices_2,
                  deg_key='two_group_deg',
                  method='wilcoxon'
                 )

check results

perform one-vs-others in a subset of groups

deg_by_subsets(adata, group_key='leiden', subset=['1','13','14'], 
               deg_key='deg_1_13_14', method='wilcoxon'
              )

check results