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.
- 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 for more information.
moscot is powered by OTT 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.
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.
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.