thesecondfox/skill

Bioinformatics Skills Collection

A curated library of 492 AI-agent skills for computational biology and bioinformatics.

Explore Domains
·
Quick Start
·
AI Agent Guide

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Table of Contents

• Overview
• Architecture
• Omics Domains
• Common Skills
• Quick Start
• Installation
• For AI Agents
• Contributing
• Star History
• License

Overview

This repository provides 492 curated bioinformatics skills designed for AI coding agents (Claude Code, Cursor, etc.). Each skill is a structured instruction set that teaches an AI agent how to perform a specific bioinformatics task — from raw data processing to publication-quality visualization.

Key Features

• 17 omics domains covering the full spectrum of modern bioinformatics
• Pipeline-oriented README in each domain, organized by analysis lifecycle
• Two-Tier architecture separating cross-domain tools from domain-specific analyses
• 30+ database connectors for PubMed, UniProt, KEGG, ClinVar, gnomAD and more
• 40+ pre-built workflows for RNA-seq, ATAC-seq, GWAS, metagenomics and more
• AI Agent Guide with routing table and orchestration protocol

Architecture

skill/
├── Common_Skills/          248 cross-domain tools
│   ├── Database access         (PubMed, UniProt, KEGG, GEO, ...)
│   ├── Visualization           (Circos, heatmaps, volcano, ...)
│   ├── Sequence operations     (I/O, format conversion, intervals)
│   ├── Statistical analysis    (experimental design, multiple testing)
│   ├── Workflow management     (Snakemake, Nextflow, CWL, WDL)
│   ├── Scientific writing      (LaTeX, PPTX, Jupyter, Quarto)
│   └── Core libraries          (scanpy, biopython, pysam, rdkit, ...)
│
├── Omics_Domains/          244 domain-specific skills
│   ├── Genomics/               (39 skills)
│   ├── Epigenomics/            (26 skills)
│   ├── Transcriptomics/        (24 skills)
│   ├── ...                     (14 more domains)
│   └── Long_Read/              (4 skills)
│
├── AI_AGENT_GUIDE.md       Instruction for AI agents
├── CHANGELOG_20260326.md   Change log
└── README.md               This file

Omics Domains

Each domain directory contains a README.md that maps skills to pipeline stages.

Common Skills

Quick Start

1. Find the right skill

User task: "Analyze my scRNA-seq data"

Step 1: Identify domain        → Single_Cell
Step 2: Read pipeline README   → Omics_Domains/Single_Cell/README.md
Step 3: Pick pipeline stage    → preprocessing → clustering → annotation
Step 4: Load skill             → bio-single-cell-preprocessing/SKILL.md

2. Skill file structure

Each skill contains at minimum a SKILL.md:

bio-single-cell-clustering/
└── SKILL.md          # Capabilities, workflow, parameters, examples

# Some skills include additional resources:
bio-aging-clocks/
├── SKILL.md          # Core documentation
├── reference.md      # API reference
└── examples/         # Runnable scripts

Installation

Clone the repository:

git clone [email protected]:thesecondfox/skill.git

For Claude Code

# Copy to Claude skills directory
cp -r skill/ ~/.claude/skills/

For Cursor

# Copy to Cursor rules directory
cp -r skill/ ~/.cursor/rules/

For AI Agents

See AI_AGENT_GUIDE.md for:

• Skill resolution protocol and domain routing table
• Loading priority rules
• Multi-skill orchestration patterns
• Common Skills category index

Contributing

Contributions are welcome! To add a new skill:

1. Fork this repository
2. Create a new directory under the appropriate location:
   • Common_Skills/ for cross-domain tools
   • Omics_Domains// for domain-specific skills
3. Add a SKILL.md following the existing format
4. Update the domain README.md to include your skill in the pipeline
5. Submit a Pull Request

Skill format

# Skill Name

## Overview
Brief description of what this skill does.

## When to Use This Skill
Conditions that trigger this skill.

## Workflow
Step-by-step analysis procedure.

## Parameters
Key parameters and their defaults.

## Examples
Runnable code examples.

Star History

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License

This project is licensed under the MIT License - see the LICENSE file for details.

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Made with Claude Code