, groups=None, filter_by='pvals_adj < 0.01', sort_by='scores', ascending=False)[source]

Extract result of in the form of marker gene data frame for specific cell groups

  • adata (AnnData) – Input dataset

  • groups (typing.Optional[typing.List[str]]) – Target groups for which markers should be extracted, by default extract all groups.

  • filter_by (str) – Marker filtering criteria (passed to pandas.DataFrame.query())

  • sort_by (str) – Column used for sorting markers

  • ascending (str) – Whether to sort in ascending order

Return type:



marker_df – Extracted marker data frame


Markers shared by multiple groups will be assign to the group with highest score.