cassiopeia.pp.filter_cells#
- cassiopeia.pp.filter_cells(molecule_table, min_umi_per_cell=10, min_avg_reads_per_umi=2.0)[source]#
Filter out cell barcodes that have too few UMIs or too few reads/UMI.
- Parameters:
- molecule_table
DataFrame A molecule table of cellBC-UMI pairs to be filtered
- min_umi_per_cell
int(default:10) Minimum number of UMIs per cell for cell to not be filtered. Defaults to 10.
- min_avg_reads_per_umi
float(default:2.0) Minimum coverage (i.e. average) reads per UMI in a cell needed in order for that cell not to be filtered. Defaults to 2.0.
- molecule_table
- Return type:
- Returns:
A filtered molecule table