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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

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- 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