| Name | CellClear JSON |
| Version |
0.0.2
JSON |
| download |
| home_page | None |
| Summary | Estimating and removing ambient expression in scRNA-seq data |
| upload_time | 2024-08-20 04:18:17 |
| maintainer | None |
| docs_url | None |
| author | WhiteRabBio |
| requires_python | >=3.9 |
| license | BSD 3-Clause License Copyright (c) 2024, WhiteRabBio Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
scrna-seq
bioinformatics
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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
Raw data
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