Multi-omic single-cell optimal transport tools
Project description
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.
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