zhoujt1994 / Fast-Higashi

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Fast-Higashi: Ultrafast and interpretable single-cell 3D genome analysis

https://www.biorxiv.org/content/10.1101/2022.04.18.488683v1

Fast-Higashi is an interpretable model that takes single-cell Hi-C (scHi-C) contact maps as input and jointly infers cell embeddings as well as meta-interactions. figs/fig1.png

Installation

We now have Fast-Higashi on conda as well!

conda install -c ruochiz fasthigashi (only for linux)

git clone https://github.com/ma-compbio/Fast-Higashi/
cd Fast-Higashi
python setup.py install

It is recommended to have pytorch installed (with CUDA support when applicable) before installing higashi.

Documentation

The input format would be exactly the same as the Higashi software. Detailed documentation will be updated here at the Higashi wiki

Tutorial

Cite

Cite our paper by

@article {Zhang2022.04.18.488683,
	author = {Zhang, Ruochi and Zhou, Tianming and Ma, Jian},
	title = {Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi},
	elocation-id = {2022.04.18.488683},
	year = {2022},
	doi = {10.1101/2022.04.18.488683},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2022/04/19/2022.04.18.488683},
	eprint = {https://www.biorxiv.org/content/early/2022/04/19/2022.04.18.488683.full.pdf},
	journal = {bioRxiv}
}

figs/Overview.png

Contact

Please contact ruochiz@andrew.cmu.edu or raise an issue in the github repo with any questions about installation or usage.

About

License:MIT License


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