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bio-reporting-jupyter-reports

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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.

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How to use this skill

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  2. Copy the prompt below and paste it into your agent.
  3. Review the proposed files and risks before you approve installation.
Prompt to paste
I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/majiayu000/claude-skill-registry/blob/HEAD/skills/data/jupyter-reports/SKILL.md

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First, summarize what it does, its dependencies, license status if identifiable, and any risks. Show the exact files you propose to add under .agents/skills/bio-reporting-jupyter-reports/. Do not write files or run scripts until I approve.

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Copying this prompt does not install or run the skill. Review third-party files before use. Codex skill guide

Jupyter Reports with Papermill

Parameterized Notebooks

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:

# Parameters (tag this cell as "parameters")
input_file = 'default.csv'
output_dir = 'results/'
fdr_threshold = 0.05

Batch Processing

import papermill as pm
from pathlib import Path

samples = ['sample1', 'sample2', 'sample3']

for sample in samples:
    pm.execute_notebook(
        'qc_template.ipynb',
        f'reports/{sample}_qc.ipynb',
        parameters={'sample_id': sample}
    )

Converting to HTML/PDF

# 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

Best Practices

  • Keep analysis code in cells, explanatory text in markdown
  • Use parameters for all configurable values
  • Include version information and timestamps
  • Clear outputs before committing to version control

Related Skills

  • reporting/quarto-reports - Alternative report format
  • reporting/rmarkdown-reports - R-based reports
  • workflows/rnaseq-to-de - Embed in workflows