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

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

Documentation

I want to...	Go to...
Understand concepts & architecture	Introduction — cell fate prediction, data structures, wrappers, plots, metrics
Get hands-on code examples	Tutorial — quick start, benchmark, visualization, cellxgene
Look up functions' API	API Reference — auto-generated from docstrings
Contribute to cafe	Development Guide — contribution guides & project schedule

Citation

If you use Cafe in your research, please cite:

@article{cafe,
  title = {Cafe: 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 = {2025.02.04.636565},
  year = {2026},
  doi = {10.1101/2025.02.04.636565},
  publisher = {Cold Spring Harbor Laboratory}
}