Cell Type Evolution Lab
Official@musserlab · United States of America
The Musser Lab investigates the origin and evolution of animal cell types.
Agent Skills by Cell Type Evolution Lab
Showing 22 vetted skills indexed across 1 GitHub repositories.
MusserLabnew-skill
Create structured Claude Code skills with SKILL.md frontmatter and body content.
MusserLabaudit
Audit CLAUDE.md and planning documents to detect drift and stale references.
MusserLabdone
Summarize session work, update planning documents, and commit changes.
MusserLabdebugging-before-patching
Diagnose errors and document root causes before proposing fixes.
MusserLabfigure-export
Export R plots as PDF, PNG, and SVG with embedded fonts.
MusserLabnew-plan
Create and register a SCREAMING_SNAKE_CASE planning document in .claude/ with a CLAUDE.md registry entry.
MusserLabquarto-docs
Standardizes Quarto QMD workflows with numbered scripts, status tracking, and BUILD_INFO provenance.
MusserLabprotein-phylogeny
Generate a reproducible protein phylogeny analysis script using MAFFT and IQ-TREE.
MusserLabgit-conventions
Standardize Git commit messages, branching, and pull request workflows.
MusserLabdata-handling
Guide data-handling best practices for R and Python data science scripts.
MusserLabnew-project
Generate a standardized project skeleton with directories, environments, and version control.
MusserLabr-renv
Manages Rocket.Chat rooms, messages, and membership with natural commands.
MusserLabconda-env
Standardize conda environment activation and package management for Python workflows.
MusserLabsecurity-setup
Configure Claude Code security protections across hooks, deny rules, and Bash scoping.
MusserLabr-plotting-style
Standardize ggplot2 plotting conventions and base themes across R projects.
MusserLabquarto-book-setup
Generate a Quarto book scaffold with GitHub Pages deployment.
MusserLabscientific-manuscript
Automate drafting and refining scientific manuscripts with narrative-first guidance.
MusserLabgene-lookup
Map gene IDs and protein accessions to gene symbols across biological databases.
MusserLabtree-formatting
Format phylogenetic trees with ggtree or iTOL layouts and overlays.
MusserLabscript-organization
Organize data science projects with numbered scripts and BUILD_INFO.txt provenance.
MusserLabfile-safety
Enforce safe file editing rules to prevent overwriting or deletion.
MusserLabpublish
Automate Quarto project publishing to GitHub Pages via quarto publish gh-pages.
Frequently Asked Questions About Cell Type Evolution Lab
FAQPage SchemaWhat specific research tasks are enabled by these capabilities?▼
These capabilities enable reproducible phylogenetic analysis, standardized ggplot2 visualization, gene ID mapping across biological databases, and the generation of scientific manuscripts using Quarto. It provides a structured environment for managing data science projects, ensuring provenance through numbered scripts and BUILD_INFO tracking.
Which personas benefit most from these research standards?▼
Computational biologists, evolutionary researchers, and data scientists working in academic or laboratory settings benefit most. These standards are designed for researchers who require rigorous version control, reproducible environment management, and standardized documentation for complex biological datasets and manuscript preparation.
What are the prerequisites for implementing these research standards?▼
Implementation requires a local environment configured with R, Quarto, and Conda for dependency management. Users should have basic familiarity with Git for version control and the specific bioinformatics packages mentioned, such as MAFFT, IQ-TREE, and ggtree, to execute the provided analysis and visualization routines.