cellrank

CellRank: dynamics from multi-view single-cell data

2.0.7

PyPI

Maintainers: 3

CellRank 2: Unified fate mapping in multiview single-cell data

.. 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.

.. important:: Please refer to our citation guide <https://github.com/theislab/cellrank/blob/main/docs/about/cite.rst>_ to cite our software correctly.

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 if you encounter a bug, need our help or just want to make a comment/suggestion.

CellRank's key applications

Estimate differentiation direction based on a varied number of biological priors, including RNA velocity (La Manno et al. (2018), Bergen et al. (2020)), any pseudotime or developmental potential, experimental time points, metabolic labels, and more.
Compute initial, terminal and intermediate macrostates.
Infer fate probabilities and driver genes.
Visualize and cluster gene expression trends.
... and much more, check out our 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/10.1038/s41592-024-02303-9 .. _documentation: https://cellrank.org

.. _issue: https://github.com/theislab/cellrank/issues/new/choose

Keywords

FAQs

What is cellrank?

Is cellrank well maintained?

Did you know?

Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.

Install