matthieuheitz / moscot

Multi-omic single-cell optimal transport tools

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 - temporal and spatio-temporal trajectory inference - spatial mapping - spatial alignment - 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 source, run:

git clone https://github.com/theislab/moscot
cd moscot
pip install -e .'[dev]'

If used with GPU, additionally run:

pip install --upgrade "jax[cuda]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

Resources

Please have a look at our documentation

Reference

Our manuscript will be available soon.