moscot 0.5.0

Multi-omic single-cell optimal transport tools

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.

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 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.

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.