lucid-coder

A Claude Code plugin for readable, reproducible R and Python in computational biology. It gives Claude one house style for analysis code and figures, 21 tested pipeline skills for single-cell and statistics work, and rules learned from your own corrections.

Docs: https://mdmanurung.github.io/lucid-coder/

Install

In Claude Code:

/plugin marketplace add mdmanurung/lucid-coder
/plugin install lucid-coder@lucid-coder

Start a new session. The rules load at session start and into every subagent.

What is inside

• Persona and rules (rules/, skills/lucid-coder/): headers, knobs at the top, checks where data enters, seeded steps, donors as the unit.
• Learned rules (/lucid-coder:learn, /lucid-coder:rules): a lasting correction becomes a rule after you approve it.
• Figure style (skills/figure-style/, templates/): one look in ggplot2, ComplexHeatmap and plotnine with plotnine-extra.
• Pipeline skills (skills/<name>/): sc-qc, sc-normalize, sc-embed, sc-annotate, sc-markers, pseudobulk-de, sc-de, variance-partition, mashr-sharing, composition, milo-da, enrichment, signature-scoring, tf-activity, gene-programs, ccc, trajectory, velocity, mofa, group-tests and longitudinal. Each is a tested script with no analysis defaults, fixed errors and a fixed output tree.

Commands

Command	Effect
/lucid-coder on, off, status	Turn the persona on or off
/lucid-coder lang r (python, both, auto)	Choose the language rules
/lucid-coder:review	Review code against the house style
/lucid-coder:align	Install the house configs into a repo

Develop

npm test                          # hooks, rules, templates
quarto preview site               # docs site

Each pipeline skill's test command is in its references/maintainer.md. See Develop for the full guide.