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+|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
+    :width: 800px
+    :align: center
+    :class: only-dark
+
+
+**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.
+
+.. |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