notebookslisted
Install: claude install-skill fmschulz/omics-skills
# Notebooks
A single skill for authoring, validating, and delivering reproducible analysis notebooks. Marimo is the default format; Jupyter is supported for existing `.ipynb` files and when a downstream tool requires JSON. Conversion between the two formats is part of this skill.
A notebook is not "done" until it has been executed end-to-end on a fresh kernel and every figure is embedded in the delivered file.
## Instructions
1. **Pick the format.**
- New notebook: write a marimo `.py` notebook. Use the canonical cell layout (one concept per cell, final expression renders, no `if` guards around outputs, no `try/except` for control flow).
- Existing `.ipynb` to extend or polish: keep it as Jupyter unless the user asks to convert.
- Conversion: see "Convert between marimo and Jupyter" below.
2. **Outline before coding.** Write the notebook plan (purpose, data sources, analysis steps, expected outputs/plots) as the first markdown cell, then implement against that plan.
3. **Keep marimo cells clean.** These are hard rules for every `.py` notebook:
- Markdown cells use one plain triple-quoted string: `mo.md(r"""...""")` or `mo.md(f"""...""")` only when interpolation is required. Put the prose directly inside the string; never paste quoted string fragments such as `" ... "` lines inside the markdown body.
- Do not leave empty generated cells, whitespace-only cells, or `@app.cell def _(): return` placeholders. Remove them before final verification.
- Do not a