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"author": "Hongyi Xin",
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"description": "# GMM-Demux \nA Gaussian Mixture Model based software for processing cell hashing data.\n\nBelow shows an example classification result. Orange dots are multi-sample multiplets.\n\n![\"GMM-Demux](\"GMM_simplified.png\")
\n\n\n## Description\nGMM-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.\n\n## Features\n* Remove cell-hashing-identifiable multiplets from the dataset.\n* Estimate the fraction of cell-hashing-unidentifiable multiplets in the remaining dataset (the RSSM value).\n\n## Example Dataset\n* An example cell hashing data is provided in the *example_input* folder. It contains the per drop HTO count matrix of a 4-sample cell hashing library prep.\n\n# Authors\n Hongyi Xin, Qi Yan, Yale Jiang, Jiadi Luo, Carla Erb, Richard Duerr, Kong Chen* and Wei Chen*\n\n# Maintainer\nHongyi Xin \n\n\n## Requirement\n\nGMM-Demux requires python3 (>3.5).\n\n## Install\n\nGMM-Demux can be directly installed from PyPi. Or it can be built and installed locally.\n\n* Install GMM-Demux from PyPi.\n```bash\npip3 install --user GMM_Demux\n```\nIf choose to install from PyPi, it is unnecessary to download GMM-Demux from github. However, we still recommend downloading the example dataset to try out GMM-Demux.\n\n* Install GMM-Demux locally using [setuptools](https://packaging.python.org/tutorials/installing-packages/) and pip3.\n```bash\ncd \npython3 setup.py sdist bdist_wheel\npip3 install --user . \n```\n\n* Post installation processes\n\nIf this is the first time you install a python3 software through pip, make sure you add the pip binary folder to your `PATH` variable.\nTypically, the pip binary folder is located at ```~/.local/bin```.\n\nTo temporarily add the pip binary folder, run the following command:\n```bash\nexport PATH=~/.local/bin:$PATH\n```\n\nTo permenantly add the pip library folder to your `PATH` variable, append the following line to your `.bashrc` file.\n```bash\nPATH=~/.local/bin:$PATH\n```\n\n## Content\n\nThe source code of GMM-Demux is supplied in the ```GMM_Demux``` folder.\n\nAn example cell hashing dataset is also provided, located in the ```example_input/outs/filtered_feature_bc_matrix``` folder.\n\n## Usage\n\nOnce installed, the github folder is no longer needed. Instead, GMM-Demux is directly accessible with the ```GMM-demux``` command.\n```bash\nGMM-demux \n```\n\n`````` is a list of strings separated by ',' without whitespace.\nFor example, there are four HTO tags in the example cell hashing dataset supplied in this repository.\nThey are **HTO_1**, **HTO_2**, **HTO_3**, **HTO_4**. The `````` variable therefore is ```HTO_1,HTO_2,_HTO_3,HTO_4```.\n\nMSM-free droplets are stored in folder *GMM_Demux_mtx* under the current directory by default.\nThe output path can also be specified through the `-o` flag.\n\n## Example Usage\nAn example cell hashing data is provided in *example_input*. can be obtained from the features.tsv file.\n```bash\nGMM-demux example_input/outs/filtered_feature_bc_matrix HTO_1,HTO_2,HTO_3,HTO_4 35685\n```\n\n are obtained from the features.tsv file. The feature.tsv file of the example cell hashing dataset is shown below.\n\n\n\n## Optional Arguments\n* -h: show help information.\n* -f FULL, --full FULL Generate the full classification report. Require a path argument.\n* -s SIMPLIFIED, --simplified SIMPLIFIED Generate the simplified classification report. Require a path argument.\n* -o OUTPUT, --output OUTPUT Specify the folder to store the result. Require a path argument.\n* -r REPORT, --report REPORT Specify the file to store summary report. Require a file argument.\n\n## Output Values\n* CellRanger MSM-free drops, in MTX format. Compatible with CellRanger 3.0.\n* Dataset summary. An example summary is shown below.\n\n\n## Output Explanation\n* MSM denotes the percentage of identified and removed multiplets among all droplets.\n* SSM denotes the percentage of unidentifiable multiplets among all droplets.\n* RSSM denotes the percentage of multiplets among the output droplets (after removing identifiable multiplets). RSSM **measures the quality of the cell hashing dataset**.\n\n## Online Cell Hashing Experiment Planner\nA GMM-Demux based online cell hashing experiment planner is publically accessible at [here](https://www.pitt.edu/~wec47/gmmdemux.html).\n\n[![\"Online](\"planner.png\")
](https://www.pitt.edu/~wec47/gmmdemux.html)\n\n\n",
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