Metadata-Version: 2.1
Name: moscot
Version: 0.1.0
Summary: Multi-omic single-cell optimal transport tools
Project-URL: Documentation, https://moscot.readthedocs.io/
Project-URL: Source, https://github.com/theislab/moscot
Project-URL: Home-page, https://github.com/theislab/moscot
Author: Dominik Klein, Giovanni Palla, Michal Klein, Zoe Piran, Marius Lange
Maintainer-email: Dominik Klein <dominik.klein@helmholtz-muenchen.de>, Giovanni Palla <giovanni.palla@helmholtz-muenchen.de>, Michal Klein <michal.klein@helmholtz-muenchen.de>
License: BSD 3-Clause License
        
        Copyright (c) 2022, Theis Lab
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License-File: LICENSE
Keywords: bio-informatics,optimal transport,single-cell
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Typing :: Typed
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Description-Content-Type: text/x-rst

|Codecov|

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 <https://ott-jax.readthedocs.io/en/latest/>`_ 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


.. |Codecov| image:: https://codecov.io/gh/theislab/moscot/branch/master/graph/badge.svg?token=Rgtm5Tsblo
    :target: https://codecov.io/gh/theislab/moscot
    :alt: Coverage
