CFDE Knowledge Center Dataset Fetcher

A small CLI and library for downloading CFDE Knowledge Center single-cell artifacts and querying gene-level log-normalized expression.

This repository contains a brief README and a docs/ directory with usage instructions, examples, and development notes. If you need detailed guidance, see docs/usage.md and docs/examples.md.

Quick links:

• Full usage: docs/usage.md
• Short examples: docs/examples.md
• API docs (Swagger UI): https://cfde.hugeampkpnbi.org/docs

Install from PyPI:

pip install cfde-kc-fetch

If you spot missing information or a confusing message in the tool, please open an issue with a minimal reproduction and the command you ran.

Development & Testing

To run tests locally:

pip install -e ".[dev]"
pytest tests/

Project layout (essential):

• cfde_kc_fetch/ — package code
• tests/ — unit tests

References

• CFDE Knowledge Center: https://cfdeknowledge.org
• API docs (Swagger UI): https://cfde.hugeampkpnbi.org/docs
• Single Cell Browser: https://cfdeknowledge.org/single-cell/

License

MIT License - See LICENSE file for details.

Contributing

Contributions are welcome! Please:

1. Fork the repository
2. Create a feature branch
3. Add tests for new functionality
4. Submit a pull request

Citation

If you use this tool in your research, please cite:

@software{cfde_kc_fetch,
  title = {CFDE Knowledge Center Dataset Fetcher},
  author = {Zeyu Yao},
  year = {2026},
  url = {https://github.com/cytronicoder/cfde-kc-fetch}
}