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Cafe: An integrated platform for exploring cell fate

Cafe Framework

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Cafe (Cellular Fate Explorer) is a modular framework to study cellular dynamics based on single-cell RNA-seq data. It provides an integrated platform for inferring, visualizing and benchmarking cell fate trajectories.

Framework

Cafe Framework

Key Applications

  • Trajectory Inference: Infer cell fate trajectories using various backend methods (including Python-based, Docker-based, and Conda-based backends).
  • Visualization: Visualize trajectories, embeddings, pseudotime, and velocity fields with high-quality plots.
  • Benchmarking: Compare different trajectory inference methods using comprehensive metrics including topology, cluster, and feature importance.
  • Data Management: Manage complex single-cell data structures with FateAnnData, extending the capabilities of AnnData for trajectory analysis.

Citation

If you use Cafe in your research, please cite:

@article{huang2025cellfateexplorer,
    title={CellFateExplorer: An integrated platform for exploring cell fate},
    author={Huang, Zhaoyang and Ma, Haonan and Peng, Yuchuan and Zhao, Chenguang and Yu, Liang},
    journal={bioRxiv},
    pages={2025--02},
    year={2025},
    publisher={Cold Spring Harbor Laboratory}
}

Contributing

We actively encourage any contribution! To get started, please check out the development document.