CellClear: Enhancing scRNA-seq Data Quality via Biologically-Informed Ambient RNA Correction

Installation

CellClear can be installed from the python repository pypi (https://pypi.org/project/CellClear/)

Running CellClear

A typical CellClear run with default settings would look like this:

CellClear correct_expression --filtered_mtx_path filtered_feature_bc_matrix --raw_mtx_path raw_feature_bc_matrix --prefix test --output .

For full usage details with additional options, see "CellClear correct_expression --help".

CellClear outputs

(1) Determine the ambient RNA expression level

(2) Give the identified ambient genes

(3) Remove the ambient RNA from each cell and output a new matrix