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284284
285- ## Real-World Research Scenarios
286285
287- ### 🔬 Scenario 1: Publishing alongside a paper
288- ```` bash
289- # Make repository public before paper submission
290- # Tag the version used in the paper
291- git tag -a v1.0-paper -m " Code for Smith et al. 2025"
292- git push origin v1.0-paper
293-
294- # Add DOI from Zenodo for citability
295- ````
296-
297- ### 🤝 Scenario 2: Multi-lab collaboration
298- ```` bash
299- # Add collaborator's fork as remote
300- git remote add collaborator https://github.com/CollabLab/CellClusterFlow.git
301-
302- # Fetch their branches
303- git fetch collaborator
304-
305- # Review their work
306- git checkout collaborator/new-algorithm
307- ````
308-
309- ### 📚 Scenario 3: Archiving for reproducibility
310- - Link GitHub repo in paper's Data Availability section
311- - Use Zenodo integration for permanent DOI
312- - Include ` environment.yml ` or ` requirements.txt ` for exact dependencies
313-
314- ---
315286
316287## Best Practices for Research Code
317288
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