bio-reporting-jupyter-reports
Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill. Use when generating automated analysis reports, running notebook-based pipelines, or creating shareable computational notebooks.
npx skills add BioTender-max/awesome-bio-agent-skills --skill jupyter-reports --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: jupyter 1.0+, papermill 2.5+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Jupyter Reports with Papermill **"Generate reproducible analysis reports"** → Execute parameterized Jupyter notebooks programmatically and export as HTML/PDF reports. - Python: `papermill.execute_notebook(input, output, parameters={...})` - CLI: `jupyter nbconvert --to html notebook.ipynb` ## Parameterized Notebooks ```python import papermill as pm # Execute notebook with parameters pm.execute_notebook( 'analysis_template.ipynb', 'output_report.ipynb', parameters={ 'input_file': 'data/counts.csv', 'condition_col': 'treatment', 'fdr_threshold': 0.05 } ) ``` ## Creating Parameterized Templates Mark a cell with the `parameters` tag in Jupyter: ```python # Parameters (tag this cell as "parameters") input_file = 'default.cs
- Version Compatibility
- Parameterized Notebooks
- Creating Parameterized Templates
- Batch Processing
- Converting to HTML/PDF
- Best Practices
- Related Skills
Single notebook jupyter nbconvert --to html report.ipynb With execution jupyter nbconvert --execute --to html report.ipynb PDF (requires pandoc + LaTeX) jupyter nbconvert --to pdf report.ipynb
What does the bio-reporting-jupyter-reports skill do?
Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill. Use when generating automated analysis reports, running notebook-based pipelines, or creating shareable computational notebooks.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill jupyter-reports --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.