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Matsen Group Claude Code Plugins

A collection of specialized agents for scientific writing, code review, and technical documentation.

Overview

This plugin collection provides specialized agents designed to enhance your development workflow, particularly for:

• Scientific writing and LaTeX documents
• Code quality and review
• Academic publishing
• Bioinformatics pipelines

Included Agents

Scientific Writing & LaTeX

• scientific-tex-editor - Expert scientific editing for LaTeX documents following best practices
• tex-grammar-checker - Meticulous grammar checking for LaTeX/TeX files
• tex-verb-tense-checker - Review LaTeX documents for verb tense consistency
• topic-sentence-stickler - Ensure strong topic sentences in paragraph structure
• pdf-proof-reader - Proofread PDF proofs from academic journals
• journal-submission-checker - Verify repositories, references, and bibliographic information

Code Quality & Review

• clean-code-reviewer - Expert code review focused on clean code principles
• code-smell-detector - Gentle code smell detection with mentoring approach
• antipattern-scanner - Scan for architectural antipatterns and violations

Specialized Tools

• snakemake-pipeline-expert - Expert guidance on Snakemake workflows
• math-pr-summarizer - Create mathematical summaries of statistical/computational PRs
• pdf-question-answerer - Analyze and answer questions about scientific PDFs

Slash Commands

/pre-pr-check

Comprehensive pre-PR quality checklist that guides you through:

• Issue compliance verification
• Code formatting and documentation checks
• Architecture review with antipattern-scanner and clean-code-reviewer agents
• Test quality validation (no fake tests allowed!)
• Static analysis (ruff, mypy, test coverage)

Run before creating any pull request to ensure code quality standards are met.

Hooks

Desktop Notifications (macOS)

Get native macOS notifications when Claude needs your input or completes tasks.

Prerequisites:

brew install terminal-notifier

Included notifications:

• 🔔 When Claude needs your input
• ✅ When a task is completed

Notifications are automatically enabled when you install the plugin (if terminal-notifier is available).

Installation

Quick Start

To install and manage plugins, use the /plugin command which opens an interactive menu:

/plugin

This will present you with options to:

• Add a plugin (enter matsengrp/plugins or https://github.com/matsengrp/plugins when prompted)
• Enable/disable installed plugins
• Reload plugins after updates
• Remove plugins

For more information about plugins:

• Official Claude Code plugins documentation
• Video overview of Claude Code plugins

Usage

Agents

These agents will be available as specialized subagents that Claude Code can invoke automatically based on your task context, or you can invoke them manually using the Task tool.

Slash Commands

Use slash commands directly in your conversation:

• /pre-pr-check - Run comprehensive pre-PR quality checklist

Structure

plugins/
├── .claude-plugin/
│   └── plugin.json          # Plugin manifest
├── agents/                   # Agent definitions
├── commands/                 # Custom slash commands
│   └── pre-pr-check.md      # Pre-PR quality checklist
├── hooks/                    # Event handlers
│   └── hooks.json           # Desktop notifications (terminal-notifier)
└── skills/                   # Agent skills (future)

Development

This plugin is designed to replace the legacy claude-code-agents repository with the new Claude Code plugin system.

License

MIT

Author

Erick Matsen & Matsen Group