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Moscot - Multiomics Single-cell Optimal Transport

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.. module:: moscot

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    :class: only-light

.. image:: _static/img/dark_mode_concept_revised.png

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:mod:`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.

Key applications

----------------

- :doc:`Trajectory inference <notebooks/tutorials/200_temporal_problem>`

  (incorporating :doc:`spatial <notebooks/tutorials/500_spatiotemporal>`

  and :doc:`lineage <notebooks/tutorials/100_lineage>` information).

- :doc:`Mapping <notebooks/tutorials/400_spatial_mapping>` cells to their spatial organisation.

- :doc:`Aligning <notebooks/tutorials/300_spatial_alignment>` spatial transcriptomics slides.

- :doc:`Translating <notebooks/tutorials/600_tutorial_translation>` modalities.

- ... and more, check out the :doc:`user guide <user_guide>` for more information.

Getting started

----------------

- Read the :doc:`user guide <user_guide>` to get a high-level overview of :mod:`moscot`.

- Take a look at our :doc:`tutorials <notebooks/tutorials/index>` to learn how to use :mod:`moscot` for data analysis.

- For more technical examples and specific use cases, check out the :doc:`examples <notebooks/examples/index>` section.

- To see :mod:`moscot` in action, read our `Klein et al., 2025`_ manuscript.

- For a high-level introduction of moscot, check out our `research briefing <https://doi.org/10.1038/d41586-025-00107-1>`_.

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.

Important resources

-------------------

.. grid:: 3

    :gutter: 1

    .. grid-item-card:: Installation

        :link: installation

        :link-type: doc

        Learn how to install :mod:`moscot`.

    .. grid-item-card:: User API

        :link: user/index

        :link-type: doc

        Find a detailed documentation of :mod:`moscot`.

    .. grid-item-card:: Contributing

        :link: contributing

        :link-type: doc

        Add a functionality or report a bug.

    .. grid-item-card:: Examples

        :link: notebooks/examples/index

        :link-type: doc

        Find brief and concise examples of :mod:`moscot`.

    .. grid-item-card:: Tutorials

        :link: notebooks/tutorials/index

        :link-type: doc

        Check out how to use :mod:`moscot` for data analysis.

    .. grid-item-card:: Manuscript

        Please have a look at `Klein et al., 2025`_ to learn more.

.. toctree::

    :maxdepth: 2

    :hidden:

    installation

    user_guide

    user/index

    developer/index

    ot_background

    notebooks/tutorials/index

    notebooks/examples/index

    contributing

    references

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    :alt: Coverage

.. |PyPI| image:: https://img.shields.io/pypi/v/moscot.svg

    :target: https://pypi.org/project/moscot/

    :alt: PyPI

.. |CI| image:: https://img.shields.io/github/actions/workflow/status/theislab/moscot/test.yml?branch=main

    :target: https://github.com/theislab/moscot/actions

    :alt: CI

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   :alt: pre-commit.ci status

.. |Docs| image:: https://img.shields.io/readthedocs/moscot

    :target: https://moscot.readthedocs.io/en/stable/

    :alt: Documentation

.. |Downloads| image:: https://static.pepy.tech/badge/moscot

    :target: https://pepy.tech/project/moscot

    :alt: Downloads

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