Real-World Research Scenarios

🔬 Scenario 1: Publishing alongside a paper

# Make repository public before paper submission
# Tag the version used in the paper
git tag -a v1.0-paper -m "Code for Smith et al. 2025"
git push origin v1.0-paper

# Add DOI from Zenodo for citability

🤝 Scenario 2: Multi-lab collaboration

# Add collaborator's fork as remote
git remote add collaborator https://github.com/CollabLab/CellClusterFlow.git

# Fetch their branches
git fetch collaborator

# Review their work
git checkout collaborator/new-algorithm

📚 Scenario 3: Archiving for reproducibility

• Link GitHub repo in paper's Data Availability section
• Use Zenodo integration for permanent DOI
• Include environment.yml or requirements.txt for exact dependencies

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