Multigrate: multiomic data integration for single-cell genomics

Multigrate: multiomic data integration for single-cell genomics#

Tests Documentation

Getting started#

Please refer to the documentation. In particular, the

and the tutorials:

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

  1. 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#

Anastasia Litinetskaya, Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, and Fabian Theis. 2022. “Integration and querying of multimodal single-cell data with PoE-VAE.” bioRxiv. 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.

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