Skills Usage Guide

📖 Table of Contents (click to expand)

• Skills Usage Guide
  • Quick Start
  • Setup & Discovery
  • Finding Skills by Use Case
  • How Skills Are Discovered and Invoked
    • For Users
    • For AI Agents
  • Contributing New Skills
  • Platform-Specific Information
    • Claude Code
    • GitHub Copilot
    • Other Agents
  • Questions?

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Quick Start

1. Browse by category in SKILLS.md to find a skill that matches your need
2. Read the skill description to understand when to use it
3. Invoke naturally: Describe what you need to your AI agent
   • Example: “Help me create a new skill”

Platform shortcuts: Optional shortcuts (like /skill-name or @workspace patterns) are documented in instructions/ for each platform.

Setup & Discovery

First time?

• See instructions/claude.md (Claude Code)
• See instructions/copilot.md (GitHub Copilot)

Understanding the design:

• See AGENTS.md for how skill discovery and invocation work

Finding Skills by Use Case

“I want to work on an R package…“ Use analyze-r-package to understand it, create-package-instructions to generate AI docs, improve-code-coverage or security-audit-r-package for quality control, and update-r-news for release notes.

“I want to create a new skill…“ Start with create-skill for guided help, then validate-skill and document-skill.

“I want to verify my setup…“ Run check-bioconductor-skills or check the instructions/ directory.

“I want to perform a Bioconductor data analysis task…“ Check the bioc-howto index for step-by-step guides and code examples.

“I want to analyze a workflow and automate it…“ Use create-skill.

“I want to ensure my skill meets standards…“ Use validate-skill iteratively until it passes.

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How Skills Are Discovered and Invoked

For Users

1. Browse SKILLS.md to understand what’s available
2. Describe your need to your AI agent in natural language
3. Agent handles the rest: Matches need, reads skill file, executes process, and outputs result

For AI Agents

1. Read SKILLS.md as the primary discovery mechanism
2. Match user intent to skill descriptions
3. Locate and read the skill file at skills/{skill-name}/SKILL.md
4. Execute using platform tools and deliver output

See AGENTS.md for the complete agent behavior standard.

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Contributing New Skills

Want to add a new skill?

1. Brainstorm: Use create-skill
2. Create: Follow guidance to create the skill file
3. Validate: Run validate-skill
4. Document: Use document-skill to update SKILLS.md
5. Test: Verify it works on your platform
6. Submit: Create a PR for review

See CONTRIBUTING.md for detailed guidelines.

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Platform-Specific Information

Claude Code

See instructions/claude.md for setup and /skill-name shortcuts.

GitHub Copilot

See instructions/copilot.md for setup and @workspace shortcuts.

Other Agents

See instructions/ for available adapters.

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Questions?

• How does skill invocation work? → See AGENTS.md
• How do I create a new skill? → Use create-skill or see CONTRIBUTING.md
• Where are the actual skill files? → skills/{skill-name}/SKILL.md
• Can I use skills on multiple platforms? → Yes! Skills are platform-agnostic
• How do I verify my setup? → Ask your agent: Do I have the Bioconductor skills? This should invoke check-bioconductor-skills if your setup is working. See instructions/ for agent-specific setup (e.g. instructions/copilot.md).
• I found an issue with a skill or want to suggest a new skill → File an issue at https://github.com/bioconductor/ai-agent-skills/issues