moscot - multi-omic single-cell optimal transport tools

moscot is a scalable framework for Optimal Transport (OT) applications in single-cell genomics. It can be used for

• 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

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

You can install moscot via:

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.

Resources

Please have a look at our documentation

Reference

Our preprint "Mapping cells through time and space with moscot" can be found here.