Jupyter Reports with Papermill

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.

majiayu000/claude-skill-registry·0installs663starsProductivity & Planning

SKILL.md

Full skill instructions

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

Install skill

Copy and run in your terminal

npx -y skills add https://github.com/majiayu000/claude-skill-registry --skill jupyter-reports

View on GitHub

skills/data/jupyter-reports/SKILL.md

More Productivity & Planning skills

View all

Productivity & Planning

brainstorming

Structured design dialogue that validates ideas before implementation begins.

295.4K 385.7K

View

Productivity & Planning

ui-ux-pro-max

Comprehensive design intelligence for web and mobile UI/UX across 10 technology stacks.

133.1K 383.9K

View

Productivity & Planning

writing-plans

Comprehensive implementation plans for multi-step tasks, breaking down specs into bite-sized, testable steps.

295.4K 268K

View

Productivity & Planning

using-superpowers

Introduction to the obra skills system with mandatory skill invocation rules and best practices.

295.4K 259.8K

View

Productivity & Planning

executing-plans

Execute a written implementation plan with critical review and task checkpoints.

295.4K 229.1K

View

Productivity & Planning

dispatching-parallel-agents

Delegate independent tasks to specialized agents working concurrently with isolated context.

295.4K 206.3K

View

Productivity & Planning

using-git-worktrees

Isolated git worktrees with smart directory selection and safety verification.

295.4K 205.2K

View

Productivity & Planning

webapp-testing

Toolkit for interacting with and testing local web applications using Playwright. Supports verifying frontend functionality, debugging UI behavior, capturing browser screenshots, and viewing browser logs.

179.7K 170.6K

View