|PyPI| |Downloads| |CI| |Docs| |Codecov| |Discourse|
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CellRank is a modular framework to study cellular dynamics based on Markov state modeling of
multi-view single-cell data. See our documentation
, and the CellRank 1
and CellRank 2 manuscript
to learn more.
See here <https://github.com/theislab/cellrank/blob/main/docs/about/cite.rst>
for how to properly cite our work.
CellRank scales to large cell numbers, is fully compatible with the scverse
ecosystem, and easy to use.
In the backend, it is powered by pyGPCCA
(Reuter et al. (2018)
). Feel
free to open an issue
or send us an email
_ if you encounter a bug, need our help or just
want to make a comment/suggestion.
La Manno et al. (2018)
, Bergen et al. (2020)
), any pseudotime or developmental potential,
experimental time points, metabolic labels, and more.documentation
_... |PyPI| image:: https://img.shields.io/pypi/v/cellrank.svg :target: https://pypi.org/project/cellrank :alt: PyPI
.. |Downloads| image:: https://static.pepy.tech/badge/cellrank :target: https://pepy.tech/project/cellrank :alt: Downloads
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.. |CI| image:: https://img.shields.io/github/actions/workflow/status/theislab/cellrank/test.yml?branch=main :target: https://github.com/theislab/cellrank/actions :alt: CI
.. |Docs| image:: https://img.shields.io/readthedocs/cellrank :target: https://cellrank.readthedocs.io/ :alt: Documentation
.. |Codecov| image:: https://codecov.io/gh/theislab/cellrank/branch/main/graph/badge.svg :target: https://codecov.io/gh/theislab/cellrank :alt: Coverage
.. _La Manno et al. (2018): https://doi.org/10.1038/s41586-018-0414-6 .. _Bergen et al. (2020): https://doi.org/10.1038/s41587-020-0591-3 .. _Reuter et al. (2018): https://doi.org/10.1021/acs.jctc.8b00079
.. _scverse: https://scverse.org/ .. _pyGPCCA: https://github.com/msmdev/pyGPCCA
.. _CellRank 1: https://www.nature.com/articles/s41592-021-01346-6 .. _CellRank 2 manuscript: https://doi.org/10.1101/2023.07.19.549685 .. _documentation: https://cellrank.org
.. _email: mailto:info@cellrank.org .. _issue: https://github.com/theislab/cellrank/issues/new/choose