Metadata-Version: 2.0
Name: GMM-Demux
Version: 0.0.1
Summary: A multiplet removal tool for processing cell hashing data
Home-page: https://github.com/CHPGenetics/GMM-demux
Author: Hongyi Xin
Author-email: gohongyi@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3
Requires-Dist: BitVector
Requires-Dist: argparse
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: scipy
Requires-Dist: statistics
Requires-Dist: tabulate

# GMM-Demux 
A Gaussian Mixture Model based software for processing cell hashing data.

Blow shows an example classification result. Orange dots are multi-sample multiplets.

![GMM-Demux example](GMM_simplified.png)

## Description
GMM-Demux removes Multi-Sample-Multiplets (MSMs) in a cell hashing dataset and estimates the fraction of Same-Sample-Multiplets (SSMs) and singlets in the remaining dataset.

# Author
 Hongyi Xin, Qi Yan, Yale Jiang, Jiadi Luo, Carla Erb, Richard Duerr, Kong Chen* and Wei Chen*

# Maintainer
Hongyi Xin <xhongyi@pitt.edu>


## Usage
```bash
python3 GMM-demux.py <cell_hashing_path> <HTO_names> <estimated_cell_num>
```
MSM-free droplets are stored in folder *GMM_Demux_mtx* by default.

## Example Usage
An example cell hashing data is provided in *example_input*. <HTO_names> can be obtained from the features.tsv file.
```bash
python3 GMM-demux.py example_input/outs/filtered_feature_bc_matrix HTO_1,HTO_2,HTO_3,HTO_4 35685
```

## Optional Arguments
* -h: show help information.
* -f FULL, --full FULL  Generate the full classification report. Require a path argument.
* -s SIMPLIFIED, --simplified SIMPLIFIED  Generate the simplified classification report. Require a path argument.
* -o OUTPUT, --output OUTPUT  Specify the folder to store the result. Require a path argument.
* -r REPORT, --report REPORT  Specify the file to store summary report. Require a file argument.

## Output values
* CellRanger MSM-free drops, in MTX format. Compatible with CellRanger 3.0.


## Online Cell Hashing Experiment Planner
A GMM-Demux based online cell hashing experiment planner is publically accessible at [link](https://www.pitt.edu/~wec47/gmmdemux.html).

![Online explanner example](planner.png)


