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+|PyPI| |Downloads| |CI| |Pre-commit| |Codecov| |Docs|
+
+Moscot - Multiomics Single-cell Optimal Transport
+=================================================
+.. module:: moscot
+
+.. image:: _static/img/light_mode_concept_revised.png
+    :width: 800px
+    :align: center
+    :class: only-light
+
+.. image:: _static/img/dark_mode_concept_revised.png
+    :width: 800px
+    :align: center
+    :class: only-dark
+
+: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
+
+
+.. |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