/multigrate

Multigrate: multiomic data integration for single-cell genomics

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

Multigrate: multiomic data integration for single-cell genomics

Tests Documentation

ICML 2021 CompBio Workshop paper is on bioarxiv.

Also see the reproducibility repo.

Getting started

Please refer to the documentation. In particular, the

Installation

You need to have Python >= 3.8, < 3.11. If you don't have Python installed, we recommend installing Miniconda.

Create a new conda environment and activate it:

conda create -n multigrate python=3.10
conda activate multigrate

There are several alternative options to install multigrate:

  1. Install the latest release from PyPI:
pip install multigrate
  1. Install the latest development version:
pip install git+https://github.com/theislab/multigrate.git@main

Release notes

See the changelog.

Contact

If you found a bug, please use the issue tracker.

Citation

If you use multigrate in your research, please consider citing

@article {Lotfollahi2022.03.16.484643,
	author = {Lotfollahi, Mohammad and Litinetskaya, Anastasia and Theis, Fabian J.},
	title = {Multigrate: single-cell multi-omic data integration},
	elocation-id = {2022.03.16.484643},
	year = {2022},
	doi = {10.1101/2022.03.16.484643},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2022/03/17/2022.03.16.484643},
	eprint = {https://www.biorxiv.org/content/early/2022/03/17/2022.03.16.484643.full.pdf},
	journal = {bioRxiv}
}