Multigrate: multiomic data integration for single-cell genomics

ICML 2021 CompBio Workshop paper is on bioarxiv.

Also see the reproducibility repo.

Getting started

Please refer to the documentation. In particular, the

• API documentation.

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}
}