musserlab
29 verified skills29 total stars
audit-project
Periodic project health check - cross-check docs, prune conventions, find drift. Use when project documentation feels stale, before milestones, or when CLAUDE.md is getting long. Do NOT load for auditing skills (use /audit-skills) or data analysis scripts (use /audit-script).
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debugging-before-patching
Systematic debugging and error diagnosis. Use when debugging errors, fixing bugs, diagnosing problems in code or data, or when the user reports something not working.
development1
gene-lookup
Look up gene or protein information from biological database IDs and accessions. Use when working with gene IDs, protein accessions, or identifiers from UniProt, Ensembl, FlyBase, WormBase, NCBI/RefSeq, or similar databases. Covers: identifying what database an ID comes from, converting IDs to gene symbols or names, retrieving protein function or annotation, batch querying APIs, and cross-referencing between databases. Use whenever someone asks "what gene is this", "look up this protein", "get info on these accessions", or needs to map between identifier systems. Also use for phylogenetic tree tip label gene name resolution.
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audit-script
Systematic audit of data analysis scripts for bugs, analytical reasoning, data handling, style, and reproducibility. Includes domain verification phase that researches tools, file formats, and methods to catch domain-specific errors (not just code bugs). Use when auditing a script, reviewing code for correctness, checking for bugs, preparing a script for publication, or when the user says "audit this script", "review this code", "check this for bugs", or "is this script correct". Three modes: thorough (collaborative section-by-section), fast (Claude-driven with discussion), and report-only. Do NOT load for quick one-off questions about a single line or function.
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cleanup-scripts
Session-scoped script cleanup for data science projects. Checks scripts/scratch/ for working files that need consolidation into .qmd scripts, flags numbered non-.qmd files in scripts/, and verifies script-output directory correspondence. Use when finishing a coding session, when scripts/scratch/ has accumulated files, or when the user says "clean up scripts", "consolidate scratch", or "check script conventions". Lightweight and fast — reads files, no expensive computation.
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audit-skills
Audit Claude Code skills for bloat, trigger accuracy, structural quality, redundancy, and pruning opportunities. Use when skills feel bloated, before publishing to lab repo, after building several new skills, when reviewing a single newly-created skill before publishing, or when the user says "audit my skills", "review skills", "check skill quality", "audit this skill", or invokes /audit-skills. Covers both user-level (~/.claude/skills/) and project-level (.claude/skills/) skills, and supports both full-library scans and single-skill reviews. Do NOT load for auditing data analysis scripts (use /audit-script) or project documentation (use /audit-project).
development1
done
Use when ending a session, wrapping up work, or when the user says "done", "wrap up", "let's commit", or "end of session". Summarizes work, updates docs, and commits.
documentation1
new-plan
Use when starting multi-script or multi-session work that needs tracking, or when the user invokes /new-plan. Creates a planning document and registers it in the project CLAUDE.md.
documentation1
learn-code
Interactive walkthrough of data analysis scripts for learning. Use when a student asks to understand a script, wants code explained, says "walk me through this", "teach me this script", "explain this code", or "what does this script do". Covers coding mechanics, script organization, and analytical reasoning as an integrated practice. Do NOT load for quick "what does this function do" questions — only for structured walkthroughs of script sections or whole scripts.
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protein-phylogeny
Protein (gene) phylogeny inference pipeline: generates a .qmd analysis script that performs alignment, optional trimming, and tree building. Use when building phylogenetic trees from protein sequences, aligning protein families, running IQ-TREE or MAFFT for phylogenetics, or when the user says "gene tree" or "protein tree." Covers single domains, whole proteins, and multi-domain proteins across deep evolutionary distances (sponges, animals, eukaryotes). Do NOT load for nucleotide-only phylogenies, species trees from concatenated matrices, or tree visualization (use tree-formatting skill for that).
development1
tree-formatting
Phylogenetic tree visualization and formatting with ggtree (R) or iTOL (web). Use when rendering a phylogenetic tree as a figure, choosing tree layout, coloring branches or labels by taxonomy, collapsing clades, displaying support values, or adding overlays to a tree. Do NOT load for tree inference (use protein-phylogeny skill) or domain annotation (future separate skill).
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deep-research-reports
Process deep research report outputs for scRNAseq cell type annotation and non-metazoan gene characterization. Use when the user invokes /process-deep-research or asks to clean, convert to PDF/HTML, parse, or compile deep research reports from ChatGPT or Claude. Handles artifact removal, PDF/HTML generation, YAML header extraction, and summary table maintenance. Supports three report types: cluster-level cell-type-annotation, family-level cell-type-annotation (WGCNA-module-organized), and nonmetazoan characterization. Detects report type automatically from query.report_type field. Works on both local macOS and HPC cluster (auto-detects quarto path and LaTeX availability).
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quarto-book-setup
Initialize a new Quarto book project with GitHub Pages. Use when creating a new documentation site, tutorial, or book.
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data-handling
Data handling best practices for R and Python data science analysis scripts. Use when writing data manipulation code, analysis pipelines, or .qmd scripts that process scientific/analytical data (e.g., filtering, joining, normalizing datasets). Do NOT load for general Python scripting, infrastructure code, or configuration management.
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new-project
Use when creating a new project, setting up a project from scratch, or when the user invokes /new-project. Scaffolds directory structure, environments, git, and Claude Code configuration. Supports data science, documentation, and general project types.
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quarto-docs
Quarto document conventions for data science analysis scripts (.qmd). Use when creating or rendering .qmd analysis scripts in data science projects with numbered scripts, status fields, git hash capture, and BUILD_INFO.txt. Do NOT load for Quarto books, websites, or documentation projects — those use standard Quarto conventions without numbered script prefixes or BUILD_INFO.txt.
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deep-research-genelist
Generate deep research prompts from scRNAseq marker gene lists for cell type annotation. Use when the user invokes /gene-list-deep-research or asks to generate a deep research prompt from a gene list (cluster markers, WGCNA module, DE gene list). Produces a research-level prompt with structured YAML header for downstream compilation across clusters.
data-ai1
conda-env
Conda environment activation for Python commands. Use when running Python scripts, pip, or conda-dependent tools.
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expression-report
Generate single-cell gene expression report scripts (.qmd) with barplots, heatmaps, and cross-analysis. Use when creating expression reports for gene sets across cell types, visualizing gene expression patterns in single-cell data, or when the user says "expression report", "gene expression barplots", "expression heatmap", or wants to visualize how a gene list is expressed across cell types. Covers both categorical gene groupings (pathway components, functional categories) and data-driven groupings (taxonomy, coexpression modules). Currently Python/scanpy/matplotlib only. Do NOT load for differential expression testing, marker gene discovery, or clustering — those are upstream analyses that produce gene lists this skill consumes.
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hpc
Yale YCRC HPC cluster reference for the Musser Lab. Use when writing SLURM batch scripts, configuring job resources, managing cluster storage, running bioinformatics tools on HPC, setting up Snakemake pipelines, or connecting to the cluster remotely (SSH setup, Positron/VS Code Remote SSH, interactive sessions). Covers McCleary, Bouchet, and Misha clusters with lab-specific storage paths, partition tables, and tool resource templates.
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new-skill
Create a new Claude Code skill with proper structure and effective description. Use when creating a new skill, or when the /done skill proposes a new skill and the user approves. Also use when refactoring CLAUDE.md content into a skill.
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r-plotting-style
R ggplot2 plotting conventions and theme. Use when creating, modifying, or styling ggplot2 plots in R, or when adjusting plot themes, colors, labels, or formatting.
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script-organization
Script organization for data science analysis projects with numbered scripts, data/outs/ directories, and reproducibility conventions. Use when creating new analysis scripts in projects that follow data science conventions (numbered XX_ prefix scripts, outs/ directories, BUILD_INFO.txt). Do NOT load for documentation projects (Quarto books), infrastructure repos, or projects without data/outs/ directory structure.
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security-setup
Configure and manage Claude Code security protections for sensitive files, credentials, and data. Use when the user invokes /security-setup to set up or modify protections against unauthorized file access, credential exposure, or sensitive data leaks.
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figure-export
Figure export conventions for publication-quality R figures (PDF/PNG/SVG). Use when saving plots to files, choosing figure formats, setting DPI or dimensions, or exporting ggplot2 or base R figures for manuscripts or Inkscape editing.
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git-conventions
Git commit practices and conventions. Use when committing changes, writing commit messages, creating branches, or making PRs.
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file-safety
File modification rules to prevent overwriting important files. Use when overwriting existing files, deleting files, or writing to directories that contain important data (data/, outs/). Also applies when moving or renaming files that other scripts depend on.
data-ai1
r-renv
R renv package management for data science projects. Use when working with renv (renv.lock, renv::restore, renv::snapshot) in R analysis projects. Do NOT load for projects that do not use R or renv.
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publish
Commit and publish Quarto project to GitHub Pages. Use when the user wants to publish changes to a Quarto book or website.
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