scanpy_plus.pp.cellbender module

scanpy_plus.pp.cellbender.cellbender(adata, expected_cells=None, total_droplets_included=None, epochs=None, use_cuda=False, fpr=None, extra_args=None)

Run CellBender remove-background via base_cli.

Parameters:

• input_path (str) – Path to raw feature-barcode matrix HDF5 file.

• output_path (str) – Output path for cleaned file.

• expected_cells (Optional[int]) – Expected number of cells.

• total_droplets_included (Optional[int]) – Number of droplets to include.

• epochs (Optional[int]) – Number of training epochs.

• use_cuda (bool) – Whether to use CUDA (GPU).

• fpr (Optional[float]) – False positive rate for cell calling.

• extra_args (list) – Any additional command-line flags (as a list).