https://github.com/theislab/moscot
Multi-omic single-cell optimal transport tools
https://github.com/theislab/moscot
optimal-transport single-cell
Last synced: 8 months ago
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Multi-omic single-cell optimal transport tools
- Host: GitHub
- URL: https://github.com/theislab/moscot
- Owner: theislab
- License: bsd-3-clause
- Created: 2021-08-23T09:44:44.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2025-10-06T20:17:04.000Z (8 months ago)
- Last Synced: 2025-10-06T22:18:35.350Z (8 months ago)
- Topics: optimal-transport, single-cell
- Language: Python
- Homepage: https://moscot.readthedocs.io/
- Size: 14.4 MB
- Stars: 174
- Watchers: 2
- Forks: 11
- Open Issues: 35
-
Metadata Files:
- Readme: README.rst
- Contributing: docs/contributing.rst
- License: LICENSE
Awesome Lists containing this project
README
|PyPI| |Downloads| |CI| |Pre-commit| |Codecov| |Docs|
Moscot - Multiomics Single-cell Optimal Transport
=======================================================
.. image:: docs/_static/img/light_mode_concept_revised.png
:width: 800px
:align: center
:class: only-light
.. image:: docs/_static/img/dark_mode_concept_revised.png
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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 `_ for more information.
**moscot** is powered by
`OTT `_ 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.
.. |Codecov| image:: https://codecov.io/gh/theislab/moscot/branch/master/graph/badge.svg?token=Rgtm5Tsblo
:target: https://codecov.io/gh/theislab/moscot
: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
.. |Pre-commit| image:: https://results.pre-commit.ci/badge/github/theislab/moscot/main.svg
:target: https://results.pre-commit.ci/latest/github/theislab/moscot/main
: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