Interpretation, Extrapolation, and Perturbation of Single cells

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🎯 Overview

A living catalogue 📚 of computational methods that attempt to identify mechanistic cause‑and‑effect links and predict responses in unobserved settings. The project curates > 100 tools, classifies them by task, and provides a browsable web interface with informative tables and technical descriptions.

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🔗 Quick Access

Resource	URL
Manuscript	Interpretation, extrapolation and perturbation of single cells, Nat Rev Genet (2026)
Documentation	https://interp-extrap-perturb.readthedocs.io/
Contribute	Contribution Guidelines - Add your method!

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🤝 Contributing

We welcome contributions! 🎉 Whether you want to:

• 🆕 Add a new method — Create a YAML file in methods/
• ✏️ Update existing methods — Edit the corresponding YAML file
• 🐛 Report issues — Open an issue on GitHub
• 💡 Suggest improvements — We're always open to ideas!

👉 Get Started: Check our 📋 Contribution Guidelines for detailed instructions.

🔄 Data flow

Automated data flow from methods/ YAML files to the rendered documentation site, as follows:

1. methods/*.yaml — canonical metadata (method, year, tasks, code link, …).

2. generate_methods.py converts YAMLs → ReStructuredText via Jinja2:

   • One overview page (methods.rst).
   • One page per task (slugified). Tasks are listed in tasklist.txt; unknown tasks raise a warning.

3. Sphinx + sphinx‑book‑theme renders the site;

4. ReadTheDocs rebuilds the Website on each push.

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graph LR
    A[🗃️ methods/*.yaml] --> B[🐍 generate_methods.py]
    B --> C[📄 docs/methods*.rst]
    C --> D[🔧 Sphinx]
    D --> E[🌐 Read the Docs]
    
    style A fill:#e1f5fe
    style B fill:#f3e5f5
    style C fill:#fff3e0
    style D fill:#e8f5e8
    style E fill:#fce4ec

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📋 Process Steps:

1. 📁 Individual YAML Files — Each method stored as methods/method_name.yaml with structured metadata
2. 🛠️ Generation Script — generate_methods.py converts YAML → ReStructuredText via Jinja2:
   • 📊 One overview page (methods.rst) with sortable table
   • 🏷️ One page per task category (auto-slugified)
   • ⚠️ Tasks validation against tasklist.txt
3. 📚 Sphinx Rendering — Uses sphinx‑book‑theme for professional styling
4. 🚀 Auto-Deployment — ReadTheDocs rebuilds on each push to main

📄 Citation

Dimitrov*, D., Schrod*, S., Rohbeck, M., and Stegle, O. Interpretation, extrapolation and perturbation of single cells. Nat Rev Genet (2026). https://doi.org/10.1038/s41576-025-00920-4

License

MIT © 2025 Daniel Dimitrov, Stefan Schrod, Martin Rohbeck, Oliver Stegle