GMM-Demux 0.0.2

A multiplet removal tool for processing cell hashing data

# 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.


## 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.

## Features * Remove cell-hashing-identifiable multiplets from the dataset. * Estimate the fraction of cell-hashing-unidentifiable multiplets in the remaining dataset (the RSSM value).

# Authors

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

# Maintainer Hongyi Xin <[e-mail]>

## Install

Install GMM-demux using [setuptools](https://packaging.python.org/tutorials/installing-packages/) and pip3.

`bash python3 setup.py sdist bdist_wheel pip3 install --user . `

## Usage `bash GMM-demux <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. * Dataset summary. An example summary is shown below. 

## 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).