CellRank

CellRank is a pyGPCCA-powered tool for analyzing cellular dynamics through Markov state modeling of single-cell data, offering insights into differentiation directions, macrostates, and gene trends in the scverse ecosystem.

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What CellRank can do for you

CellRank: Dynamics from Multi-View Single-Cell Data

Description

CellRank is a modular framework designed to analyze cellular dynamics through Markov state modeling of multi-view single-cell data. It is fully compatible with the scverse ecosystem and leverages pyGPCCA for backend operations. The tool is essential for estimating differentiation directions based on various biological priors, computing macrostates, inferring fate probabilities and driver genes, and visualizing gene expression trends.

License

The project operates under the BSD-3-Clause license, promoting open redistribution and usage with or without modifications.

Documentation

Detailed guidance and information are available in the official documentation, facilitating a deeper understanding of CellRank's applications and functionalities.

Publication

The CellRank tool and its methodologies are detailed in two manuscripts referred to as "CellRank 1" and "CellRank 2." To learn more and for proper citation, refer to the manuscripts section on the GitHub page.

Contributors

The main contributors to the CellRank project are the members of the Theis Lab. You can find more about the team and their contributions on the GitHub page.

Key Applications

  • Estimation of differentiation directions based on a variety of biological priors.
  • Computation of initial, terminal, and intermediate macrostates.
  • Inference of fate probabilities and driver genes.
  • Sophisticated visualization and clustering of gene expression trends.

Keywords

  • Cellular Dynamics
  • Markov State Modeling
  • Single-Cell Data
  • PyGPCCA
  • Scverse Ecosystem
  • Gene Expression Trend Visualization

Contact

For bugs, help, or suggestions, feel free to open an issue or reach out via email at info@cellrank.org.
Should you have any specific inquiries regarding CellRank, please do not hesitate to reach out to Philipp Weiler at philipp.weiler@helmholtz-munich.de.

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Participating organisations

Helmholtz Zentrum München
Mem
University of Tübingen
Zuse Institute Berlin
German Center for Diabetes Research
Fre

Contributors