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Moscot - Multiomics Single-cell Optimal Transport

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moscot is a framework for Optimal Transport (OT) applications in single-cell genomics. It scales to large datasets and can be used for a variety of applications across different modalities.

moscot's key applications

• 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.
• ... and more, check out the documentation <https://moscot.readthedocs.io>_ for more information.

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

Install moscot by running::

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.

Citing moscot

If you find a model useful for your research, please consider citing the Klein et al., 2025_ manuscript as well as the publication introducing the model, which can be found in the corresponding documentation.

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.. _Klein et al., 2025: https://www.nature.com/articles/s41586-024-08453-2