Multi-omic single-cell optimal transport tools
Project description
moscot - multi-omic single-cell optimal transport tools
moscot is a general framework to apply tools from optimal transport to time-course single-cell data. It supports:
single-cell RNA-seq and ATAC-seq data (paired and unpaired)
single-cell lineage-traced data (prospective and retrospective)
while scaling to large cell numbers. In the backend, moscot is powered by OTT which is a Jax-based optimal transport toolkit that supports just-in-time compilation, automatic differentiation and linear memory complexity for OT problems.
Installation
In order to install moscot, run:
git clone https://github.com/theislab/moscot cd moscot pip install -e.'[dev]' pre-commit install
for pre-commit you might have to install prettier with conda: conda install -c conda-forge prettier.
If used with GPU, additionally run:
pip install --upgrade "jax[cuda]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
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