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.
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
Please have a look at our documentation
Our manuscript will be available soon.