|PyPI| |Downloads| |CI| |Docs| |Codecov| |Discourse|
.. image:: docs/_static/img/light_mode_overview.png#gh-light-mode-only :width: 600px :align: center :class: only-light
.. image:: docs/_static/img/dark_mode_overview.png#gh-dark-mode-only :width: 600px :align: center
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
.. |Discourse| image:: https://img.shields.io/discourse/posts?color=yellow&logo=discourse&server=https%3A%2F%2Fdiscourse.scverse.org :target: https://discourse.scverse.org/c/ecosystem/cellrank/ :alt: Discourse
.. |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
FAQs
CellRank: dynamics from multi-view single-cell data
We found that cellrank demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 3 open source maintainers collaborating on the project.
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