Multigrate: multiomic data integration for single-cell genomics

Getting started

Please refer to the documentation. In particular, the

• API documentation

and the tutorials:

• Paired integration and query-to-reference mapping
• Trimodal integration and query-to-reference mapping

Installation

You need to have Python 3.10 or newer installed on your system. We recommend installing Mambaforge.

To create and activate a new environment:

mamba create --name multigrate python=3.10
mamba activate multigrate

Next, there are several alternative options to install multigrate:

1. Install the latest release of multigrate from PyPI:

pip install multigrate

2. Or 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

Multigrate: Single-Cell Multi-Omic Data Integration

Mohammad Lotfollahi, Anastasia Litinetskaya, and Fabian J. Theis. 2022. 2024. bioRxiv. [https://doi.org/10.1101/2022.03.16.484643][https://doi.org/10.1101/2022.03.16.484643].

Reproducibility

Code and notebooks to reproduce the results from the paper are available at https://github.com/theislab/multigrate_reproducibility.