Estimating and removing ambient expression in scRNA-seq data
Project description
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
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