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Filter marker tables by AUC and adjusted p-value, with exact p-values for small groups - #24
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… for small groups The default `min_score=0.25` filter depended on the number of groups and on group size: 56 of 60 groups of a fine clustering returned no markers, and LILRA4 in pDCs (AUC 1.0) scored 0.125.
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The default
min_score=0.25filter depended on the number of groups and on group size: 56 of 60 groups of a fine clustering returned no markers, and LILRA4 in pDCs (AUC 1.0) scored 0.125.Changes
markers.loadandmarkers.export_csvkeep rows with AUC at least 0.6, adjusted p-value at most 0.05, and expressing fraction at least 0.2;min_scoredefaults to None, andsort_byorders rows.neg_log10_p_value, and groups that can be split from the other cells in at most 100,000 ways get exact p-values.compare.compute_bulkdrops columns without cells (or keeps them as NaN), can return each column's cell count, and validates its options.run_marker_search; tables of revision 1 still load under an explicit policy.Behaviour changes
min_auc=0.8for short lists.