Metadata-Version: 2.1
Name: CellClear
Version: 0.0.3
Summary: Estimating and removing ambient expression in scRNA-seq data
Author: WhiteRabBio
License: BSD 3-Clause License
        
        Copyright (c) 2024, WhiteRabBio
        
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Keywords: scRNA-seq,bioinformatics
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas==2.2.2
Requires-Dist: numpy==1.26.4
Requires-Dist: scipy==1.13.0
Requires-Dist: scanpy==1.9.3
Requires-Dist: leidenalg==0.10.1
Requires-Dist: anndata==0.8.0
Requires-Dist: scikit-learn==1.4.2
Requires-Dist: statsmodels==0.14.1
Requires-Dist: statannot==0.2.3
Requires-Dist: seaborn==0.11.2

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

<img src="https://github.com/WhiteRabBio/CellClear/blob/main/method.png" width="1000">



## 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:

```python
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

