Moscot - Multiomics Single-cell Optimal Transport¶

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¶

Trajectory inference (incorporating spatial and lineage information).
Mapping cells to their spatial organisation.
Aligning spatial transcriptomics slides.
Translating modalities.
… and more, check out the user guide for more information.

Getting started¶

Read the user guide to get a high-level overview of moscot.
Take a look at our tutorials to learn how to use moscot for data analysis.
For more technical examples and specific use cases, check out the examples section.
To see 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.