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moscot - multi-omic single-cell optimal transport tools

moscot is a scalable framework for Optimal Transport (OT) applications in single-cell genomics. It can be used for

• trajectory inference (incorporating spatial and lineage information)
• mapping cells to their spatial organisation
• aligning spatial transcriptomics slides
• translating modalities
• prototyping of new OT models in single-cell genomics

moscot is powered by OTT <https://ott-jax.readthedocs.io>_ which is a JAX-based Optimal Transport toolkit that supports just-in-time compilation, GPU acceleration, automatic differentiation and linear memory complexity for OT problems.

Installation

You can install moscot via::

pip install moscot

In order to install moscot from in editable mode, run::

git clone https://github.com/theislab/moscot
cd moscot
pip install -e .

For further instructions how to install jax, please refer to https://github.com/google/jax.

Resources

Please have a look at our documentation <https://moscot.readthedocs.io>_

Reference

Our preprint "Mapping cells through time and space with moscot" can be found here <https://www.biorxiv.org/content/10.1101/2023.05.11.540374v1>_.

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