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https://github.com/waldronlab/ai-agent-skills

A collection of AI agent skills relevant to our work, including analysis and development of R/Bioconductor packages + statistical and bioinformatic analysis.
https://github.com/waldronlab/ai-agent-skills

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A collection of AI agent skills relevant to our work, including analysis and development of R/Bioconductor packages + statistical and bioinformatic analysis.

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README 

          
# waldronlab AI Agent Skills



A collection of agent-agnostic skills and instructions for AI assistants (Claude Code, GitHub Copilot, and future platforms) working on projects relevant to the Waldron Lab at CUNY SPH. This repository provides domain-specific knowledge to help AI agents understand our codebases, workflows, and standards.



## What are AI Agent Skills?



Skills are structured instructions that teach AI agents about:

- Package structures and conventions

- Analysis workflows and best practices

- Data types and their handling

- Testing and documentation standards

- Organization-wide patterns



With these skills, AI agents can:

- Generate appropriate documentation

- Follow Bioconductor coding standards

- Suggest context-aware improvements

- Understand domain-specific patterns

- Provide better assistance on complex tasks



## Agent-Agnostic Design



Skills in this repository are **agent-agnostic** by design. They work across multiple AI agents through natural language invocation:



- **Canonical invocation**: Natural language matching skill descriptions

- **Optional shortcuts**: Platform adapters document conveniences (slash commands, @workspace patterns)

- **Single source**: One skill works everywhere without duplication

- **Portable**: Skills adapt to any compliant agent platform



See [AGENTS.md](AGENTS.md) for how agent behavior and skill discovery work. See [SKILL_STANDARD.md](SKILL_STANDARD.md) for technical format details.



## Quick Start



### 1. Find Skills



Browse [SKILLS.md](SKILLS.md) to see all available skills organized by category and use case.



### 2. Invoke Naturally



Describe what you need in natural language:

- "Help me create a new skill"

- "Analyze this R package"

- "Create .github/instructions for this package"



Your AI agent will match your request to the appropriate skill and execute it.



### 3. Optional Platform Shortcuts



If you prefer shortcuts:

- **Claude Code**: `/skill-name` slash commands (see [instructions/claude.md](instructions/claude.md))

- **GitHub Copilot**: `@workspace` patterns (see [instructions/copilot.md](instructions/copilot.md))



But natural language works everywhere.



## Available Skills



See [SKILLS.md](SKILLS.md) for the complete skill catalog organized by category and use case.



**Skill domains:**

- **Meta** - Repository infrastructure (skill creation, validation, documentation)

- **R/Bioconductor** - Package analysis and documentation generation

- **Metagenomics** (Planned)

- **Statistical Methods** (Planned)



## Installation



See the appropriate guide for your platform:

- **Claude Code**: [instructions/claude.md](instructions/claude.md)

- **GitHub Copilot**: [instructions/copilot.md](instructions/copilot.md)

- **Google Gemini**: [instructions/gemini.md](instructions/gemini.md)

- **Other agents**: [AGENTS.md](AGENTS.md) for compliance requirements



Each guide includes complete setup instructions specific to that platform.



### Verify Installation



Ask your agent:

- "Do I have the waldronlab skills?"

- "What waldronlab skills are available?"



The agent should list the installed skills.



## Usage Examples



### Creating R Package Instructions



Natural language invocation (works everywhere):

```

"Create .github/instructions for this R package"

```



Or use optional shortcuts:

- Claude Code: `/create-package-instructions`

- GitHub Copilot: `@workspace Create .github/instructions`



### Analyzing an R Package



Natural language invocation:

```

"Analyze this R package"

"What type of R package is this?"

```



Or use optional shortcuts:

- Claude Code: `/analyze-r-package`

- GitHub Copilot: `@workspace analyze this package`



### Creating a New Skill



Natural language invocation:

```

"Help me create a new skill for [purpose]"

```



Or use optional shortcuts:

- Claude Code: `/create-skill`

- GitHub Copilot: `@workspace create a new skill`



See [SKILLS.md](SKILLS.md) for all available skills and invocation examples.



## Repository Structure



```

ai-agent-skills/

├── README.md                      # This file

├── LICENSE                        # MIT License

├── AGENTS.md                      # Agent behavior standard (how discovery works)

├── SKILLS.md                      # Human-readable skill index (what skills exist)

├── SKILL_STANDARD.md              # Technical format spec (how to format skills)

├── CONTRIBUTING.md                # Contribution guidelines

├── CHANGELOG.md                   # Version history and release notes

│

├── skills/                        # All skills (flat structure)

│   ├── {skill-name}/              # Each skill in its own directory

│   │   ├── SKILL.md               # Skill documentation (required)

│   │   ├── templates/             # Optional supporting files

│   │   └── examples/              # Optional examples

│   └── ... (see SKILLS.md for complete list)

│

└── instructions/                  # Platform adapters (thin wrappers)

    ├── README.md                  # Adapter purpose and requirements

    ├── claude.md                  # Claude Code setup and shortcuts

    ├── copilot.md                 # GitHub Copilot setup and shortcuts

    └── gemini.md                  # Google Gemini (placeholder)

```



## Key Documentation



- **[AGENTS.md](AGENTS.md)** - How agents discover and invoke skills (mandatory behavior)

- **[SKILLS.md](SKILLS.md)** - Complete skill catalog organized by domain

- **[SKILL_STANDARD.md](SKILL_STANDARD.md)** - Technical format for creating skills

- **[CONTRIBUTING.md](CONTRIBUTING.md)** - How to contribute new skills or improvements

- **[CHANGELOG.md](CHANGELOG.md)** - Version history and release notes

- **[instructions/](instructions/)** - Platform-specific setup and shortcuts



## Examples



See [skills/create-package-instructions/examples/](skills/create-package-instructions/examples/) for complete examples of generated instructions from real waldronlab packages:



- **data-package-parquet** - parkinsonsMetagenomicData with remote parquet access via DuckDB

- More examples coming soon...



## Contributing



We welcome contributions! See [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.



### Adding New Skills



**Quick start**: Use the `create-skill` skill to get guided help!



Natural language: "Help me create a new skill for [purpose]"



Or manually:

1. Create directory: `skills/{skill-name}/`

2. Create file: `skills/{skill-name}/SKILL.md`

3. Follow the [Agent Skills Standard Format](SKILL_STANDARD.md)

4. Include YAML frontmatter with required fields (no `platforms:` or `triggers:`)

5. Write platform-agnostic core logic

6. Run `validate-skill` to check standards compliance

7. Run `document-skill` to update SKILLS.md automatically

8. Test on multiple platforms

9. Submit PR for review



### Adding New Domains



If you have a new category of skills:



1. Create skills with the new `category:` value

2. Add domain description to [SKILLS.md](SKILLS.md)

3. Include at least one working skill with examples

4. Submit PR for review



## Maintenance



### Ownership



Domain maintainers are responsible for:

- Reviewing PRs for their skills

- Keeping skills up-to-date

- Testing on supported platforms

- Responding to issues



### Version Compatibility



We aim to keep skills compatible with:

- **Claude Code**: Latest stable version

- **GitHub Copilot**: Latest VS Code extension

- **R/Bioconductor**: Current release and devel



Breaking changes are documented in [CHANGELOG.md](CHANGELOG.md).



## Support and Feedback



- **Issues**: Report bugs or request features via [GitHub Issues](https://github.com/waldronlab/ai-agent-skills/issues)

- **Discussions**: Ask questions in [GitHub Discussions](https://github.com/waldronlab/ai-agent-skills/discussions)

- **Skills Check**: Use `check-waldronlab-skills` to verify your setup



## License



MIT License - see [LICENSE](LICENSE) for details.



## Acknowledgments



These skills are developed and maintained by the waldronlab at CUNY SPH and collaborators to make AI agents more effective collaborators.



---



**Version**: 2.0.0 (agent-agnostic)

**Last Updated**: 2026-04-03