cafe-release 0.2.1rc1

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Cafe: An integrated platform for exploring cell fate

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

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.

Documentation

Comprehensive documentation is available at here, including installation, tutorial, API and so on.

Project Schedule

• Main framework code
• Document construction: instruction, tutorial, API
• Data module: FateAnnData data structure, data collection.
• Methods module: 4 backends, trajectory methods for 8 wrappers.
• Benchmark: Comprehensive metrics and benchmarking.
• Plot: Beautiful plotting capabilities.
• Downstream analysis: Interactive web platform, driver gene, and GRN 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}
}