lucid-coder
Readable, reproducible R and Python for computational biology, as a Claude Code plugin
lucid-coder makes Claude write analysis code the way a careful computational biologist does. Every session gets one house style for scripts and figures. Standard analyses run through tested scripts instead of fresh code. Your own corrections become rules that last.
Install
Run these in Claude Code:
/plugin marketplace add mdmanurung/lucid-coder
/plugin install lucid-coder@lucid-coderStart a new session. A status line reads “Loading lucid-coder…” when the rules load.
To try a local checkout without installing it:
claude --plugin-dir /path/to/lucid-coderWhat you get
| Part | What it does | Page |
|---|---|---|
| Persona | Injects the house rules at every session start and into every subagent | Persona and rules |
| Learned rules | Saves a lasting correction (“always use |>”) as a rule, after you approve it |
Persona and rules |
| Figure style | One look for every scientific figure in ggplot2, ComplexHeatmap and plotnine, with tested templates | Figures |
| Pipeline skills | 21 tested scripts for single-cell and statistics analyses, from QC to MOFA | Pipeline skills |
Quick start
Ask for analysis work as usual. The persona applies on its own:
Write a script that sums raw counts per donor for CD14+ monocytes and runs DESeq2, stim vs ctrl.
For a standard analysis, Claude picks the matching pipeline skill. It asks for each analysis parameter instead of guessing it:
Run pseudobulk DE on
data/kang.h5adfor CD14+ monocytes.
Claude then asks for the design, contrast, filters, cut-offs, seed, context and gene-id column. To see a skill work without your data, ask for its demo:
Run the pseudobulk-de demo.
Commands
| Command | Effect |
|---|---|
/lucid-coder status |
Show whether the persona is on |
/lucid-coder off, /lucid-coder on |
Turn the persona off or on |
/lucid-coder lang r (python, both, auto) |
Choose which language rules load |
/lucid-coder nudge off |
Stop the one-line “save this as a rule?” offer |
/lucid-coder:learn |
Save a correction as a rule |
/lucid-coder:rules |
List, approve, retire or trust rules |
/lucid-coder:review |
Review code against the house style; writes nothing |
/lucid-coder:align |
Install the house configs (air, ruff, lintr, palettes) into a repo, one diff at a time |