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It scales to large datasets and can be used for a\nvariety of applications across different modalities.\n\nmoscot's key applications\n---------------------------\n- Trajectory inference (incorporating spatial and lineage information).\n- Mapping cells to their spatial organisation.\n- Aligning spatial transcriptomics slides.\n- Translating modalities.\n- prototyping of new OT models in single-cell genomics.\n- ... and more, check out the `documentation \u003chttps://moscot.readthedocs.io\u003e`_ for more information.\n\n\n**moscot** is powered by\n`OTT \u003chttps://ott-jax.readthedocs.io\u003e`_ which is a JAX-based Optimal\nTransport toolkit that supports just-in-time compilation, GPU acceleration, automatic\ndifferentiation and linear memory complexity for OT problems.\n\nInstallation\n------------\nInstall **moscot** by running::\n\n    pip install moscot\n\nIn order to install **moscot** from in editable mode, run::\n\n    git clone https://github.com/theislab/moscot\n    cd moscot\n    pip install -e .\n\nFor further instructions how to install jax, please refer to https://github.com/google/jax.\n\nCiting moscot\n-------------\nIf you find a model useful for your research, please consider citing the `Klein et al., 2025`_ manuscript as\nwell as the publication introducing the model, which can be found in the corresponding documentation.\n\n.. |Codecov| image:: https://codecov.io/gh/theislab/moscot/branch/master/graph/badge.svg?token=Rgtm5Tsblo\n    :target: https://codecov.io/gh/theislab/moscot\n    :alt: Coverage\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/moscot.svg\n    :target: https://pypi.org/project/moscot/\n    :alt: PyPI\n\n.. |CI| image:: https://img.shields.io/github/actions/workflow/status/theislab/moscot/test.yml?branch=main\n    :target: https://github.com/theislab/moscot/actions\n    :alt: CI\n\n.. |Pre-commit| image:: https://results.pre-commit.ci/badge/github/theislab/moscot/main.svg\n   :target: https://results.pre-commit.ci/latest/github/theislab/moscot/main\n   :alt: pre-commit.ci status\n\n.. |Docs| image:: https://img.shields.io/readthedocs/moscot\n    :target: https://moscot.readthedocs.io/en/stable/\n    :alt: Documentation\n\n.. |Downloads| image:: https://static.pepy.tech/badge/moscot\n    :target: https://pepy.tech/project/moscot\n    :alt: Downloads\n\n.. _Klein et al., 2025: https://www.nature.com/articles/s41586-024-08453-2\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fmoscot","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fmoscot","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fmoscot/lists"}