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Moscot - Multiomics Single-cell Optimal Transport
: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.
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.