| Name | cellrank JSON |
| Version |
2.0.4
JSON |
| download |
| home_page | None |
| Summary | CellRank: dynamics from multi-view single-cell data |
| upload_time | 2024-04-08 14:22:09 |
| maintainer | None |
| docs_url | None |
| author | Marius Lange, Michal Klein, Philipp Weiler |
| requires_python | >=3.8 |
| license | BSD 3-Clause License Copyright (c) 2019, Theis Lab All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
single-cell
bio-informatics
rna velocity
markov chain
gpcca
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
|PyPI| |Downloads| |CI| |Docs| |Codecov| |Discourse|
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.
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.
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/10.1101/2023.07.19.549685
.. _documentation: https://cellrank.org
.. _email: mailto:info@cellrank.org
.. _issue: https://github.com/theislab/cellrank/issues/new/choose
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