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Multi-omic single-cell optimal transport tools

Home Page: https://moscot-tools.org

License: BSD 3-Clause "New" or "Revised" License

Python 100.00%

moscot's Introduction

PyPI Downloads CI pre-commit.ci status Coverage Documentation

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.

moscot's People

Contributors

mucdk avatar michalk8 avatar giovp avatar arinadanilina avatar pre-commit-ci[bot] avatar selmanozleyen avatar marius1311 avatar zoepiran avatar nosander avatar weilerp avatar

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