Appendix E — Lab Skills Reference
This appendix lists all Claude Code skills available in the Musser Lab toolkit. Install them from MusserLab/lab-claude-skills — see The Musser Lab Toolkit for installation instructions.
E.1 Background Skills
Background skills load automatically based on context. You don’t invoke them — Claude detects when they’re relevant and follows their instructions.
| Skill | Description |
|---|---|
data-handling |
Shows data dimensions after loading, validates joins, asks before analytical decisions |
debugging-before-patching |
Diagnoses root causes before fixing; never blind-patches symptoms |
file-safety |
Prevents overwriting raw data (data/) and important files |
git-conventions |
Co-author line in commits, reviews staged changes, avoids committing secrets |
conda-env |
Sources conda before activation (required in non-interactive shells) |
r-renv |
Explains renv warnings, reminds about renv::snapshot() after installs |
r-plotting-style |
Lab ggplot2 theme: theme_classic(), ggrepel labels, consistent sizing |
quarto-docs |
QMD analysis script conventions: status fields, git hash, BUILD_INFO.txt |
script-organization |
Numbered scripts (01_, 02_), outs/ directories, lifecycle status |
figure-export |
Publication-quality figure saving: PDF (cairo_pdf), PNG (300 DPI), SVG (svglite) |
scientific-manuscript |
Writing guidance for high-impact journals (narrative structure, prose style) |
protein-phylogeny |
Generates phylogenetics pipeline: MAFFT alignment, optional trimming, IQ-TREE |
gene-lookup |
Looks up gene/protein info from database IDs (UniProt, Ensembl, FlyBase, etc.) |
tree-formatting |
Phylogenetic tree visualization with ggtree: layout, coloring, clade collapsing |
E.2 Slash Commands
Slash commands are invoked explicitly by typing /command in the Claude Code chat.
| Command | Description |
|---|---|
/done |
End-of-session wrap-up: summarize work, check renv, offer to commit |
/new-project |
Scaffold a complete project: directories, conda env, renv, CLAUDE.md, git |
/new-plan |
Create a planning document in .claude/ and register it in CLAUDE.md |
/publish |
Commit changes and publish Quarto book/website to GitHub Pages |
/quarto-book-setup |
Initialize a new Quarto book project with GitHub Pages deployment |
/audit |
Project health check: cross-check docs, prune conventions, find drift |
/new-skill |
Create a new Claude Code skill with proper structure and description |
/security-setup |
Configure security protections for sensitive files and credentials |