cassiopeia.pp.filter_cells

cassiopeia.pp.filter_cells(molecule_table, min_umi_per_cell=10, min_avg_reads_per_umi=2.0)

Filter out cell barcodes that have too few UMIs or too few reads/UMI

Parameters

molecule_table : DataFrameDataFrame

A molecule table of cellBC-UMI pairs to be filtered

min_umi_per_cell : intint (default: 10)

Minimum number of UMIs per cell for cell to not be filtered

min_avg_reads_per_umi : floatfloat (default: 2.0)

Minimum coverage (i.e. average) reads per UMI in a cell needed in order for that cell not to be filtered

Return type

DataFrameDataFrame

Returns

A filtered molecule table

cassiopeia.pp.filter_molecule_table cassiopeia.pp.filter_umis