Claude Scientific Skills

A comprehensive collection of 140 ready-to-use scientific skills for Claude, created by K-Dense. Transform Claude into your AI research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond.

Looking for the full AI co-scientist experience? Try K-Dense Web for 200+ skills, cloud compute, and publication-ready outputs.

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K-Dense Web - The Full Experience

Want 10x the power with zero setup? K-Dense Web is the complete AI co-scientist platform—everything in this repo, plus:

| Feature | This Repo | K-Dense Web | |---------|-----------|-------------| | Scientific Skills | 140 skills | 200+ skills (exclusive access) | | Setup Required | Manual installation | Zero setup — works instantly | | Compute | Your machine | Cloud GPUs & HPC included | | Workflows | Basic prompts | End-to-end research pipelines | | Outputs | Code & analysis | Publication-ready figures, reports & papers | | Integrations | Local tools | Lab systems, ELNs, cloud storage |

Researchers at Stanford, MIT, and leading pharma companies use K-Dense Web to accelerate discoveries.

Get $50 in free credits — no credit card required.

Learn more at k-dense.ai | Read our detailed comparison →

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These skills enable Claude to seamlessly work with specialized scientific libraries, databases, and tools across multiple scientific domains:

• 🧬 Bioinformatics & Genomics - Sequence analysis, single-cell RNA-seq, gene regulatory networks, variant annotation, phylogenetic analysis
• 🧪 Cheminformatics & Drug Discovery - Molecular property prediction, virtual screening, ADMET analysis, molecular docking, lead optimization
• 🔬 Proteomics & Mass Spectrometry - LC-MS/MS processing, peptide identification, spectral matching, protein quantification
• 🏥 Clinical Research & Precision Medicine - Clinical trials, pharmacogenomics, variant interpretation, drug safety, clinical decision support, treatment planning
• 🧠 Healthcare AI & Clinical ML - EHR analysis, physiological signal processing, medical imaging, clinical prediction models
• 🖼️ Medical Imaging & Digital Pathology - DICOM processing, whole slide image analysis, computational pathology, radiology workflows
• 🤖 Machine Learning & AI - Deep learning, reinforcement learning, time series analysis, model interpretability, Bayesian methods
• 🔮 Materials Science & Chemistry - Crystal structure analysis, phase diagrams, metabolic modeling, computational chemistry
• 🌌 Physics & Astronomy - Astronomical data analysis, coordinate transformations, cosmological calculations, symbolic mathematics, physics computations
• ⚙️ Engineering & Simulation - Discrete-event simulation, multi-objective optimization, metabolic engineering, systems modeling, process optimization
• 📊 Data Analysis & Visualization - Statistical analysis, network analysis, time series, publication-quality figures, large-scale data processing, EDA
• 🧪 Laboratory Automation - Liquid handling protocols, lab equipment control, workflow automation, LIMS integration
• 📚 Scientific Communication - Literature review, peer review, scientific writing, document processing, posters, slides, schematics, citation management
• 🔬 Multi-omics & Systems Biology - Multi-modal data integration, pathway analysis, network biology, systems-level insights
• 🧬 Protein Engineering & Design - Protein language models, structure prediction, sequence design, function annotation
• 🎓 Research Methodology - Hypothesis generation, scientific brainstorming, critical thinking, grant writing, scholar evaluation

Transform Claude Code into an 'AI Scientist' on your desktop!

⭐ If you find this repository useful, please consider giving it a star! It helps others discover these tools and encourages us to continue maintaining and expanding this collection.

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📦 What's Included

This repository provides 140 scientific skills organized into the following categories:

• 28+ Scientific Databases - Direct API access to OpenAlex, PubMed, bioRxiv, ChEMBL, UniProt, COSMIC, ClinicalTrials.gov, and more
• 55+ Python Packages - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioPython, BioServices, PennyLane, Qiskit, and others
• 15+ Scientific Integrations - Benchling, DNAnexus, LatchBio, OMERO, Protocols.io, and more
• 30+ Analysis & Communication Tools - Literature review, scientific writing, peer review, document processing, posters, slides, schematics, and more
• 10+ Research & Clinical Tools - Hypothesis generation, grant writing, clinical decision support, treatment plans, regulatory compliance

Each skill includes:

• ✅ Comprehensive documentation (SKILL.md)
• ✅ Practical code examples
• ✅ Use cases and best practices
• ✅ Integration guides
• ✅ Reference materials

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📋 Table of Contents

• What's Included
• Why Use This?
• Getting Started
  • Claude Code
  • Cursor IDE
  • Any MCP Client
• Support Open Source
• Prerequisites
• Quick Examples
• Use Cases
• Available Skills
• Contributing
• Troubleshooting
• FAQ
• Support
• Join Our Community
• Citation
• License

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🚀 Why Use This?

⚡ Accelerate Your Research

• Save Days of Work - Skip API documentation research and integration setup
• Production-Ready Code - Tested, validated examples following scientific best practices
• Multi-Step Workflows - Execute complex pipelines with a single prompt

🎯 Comprehensive Coverage

• 140 Skills - Extensive coverage across all major scientific domains
• 28+ Databases - Direct access to OpenAlex, PubMed, bioRxiv, ChEMBL, UniProt, COSMIC, and more
• 55+ Python Packages - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioServices, PennyLane, Qiskit, and others

🔧 Easy Integration

• One-Click Setup - Install via Claude Code or MCP server
• Automatic Discovery - Claude automatically finds and uses relevant skills
• Well Documented - Each skill includes examples, use cases, and best practices

🌟 Maintained & Supported

• Regular Updates - Continuously maintained and expanded by K-Dense team
• Community Driven - Open source with active community contributions
• Enterprise Ready - Commercial support available for advanced needs

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🎯 Getting Started

Choose your preferred platform to get started:

🖥️ Claude Code (Recommended)

📚 New to Claude Code? Check out the Claude Code Quickstart Guide to get started. When using Claude Code please use the Skills as a plugin. Do not use the MCP server below.

Step 1: Install Claude Code

macOS:

curl -fsSL https://claude.ai/install.sh | bash

Windows:

irm https://claude.ai/install.ps1 | iex

Step 2: Register the Marketplace

In Claude Code, run the following command:

/plugin marketplace add K-Dense-AI/claude-scientific-skills

Step 3: Install the Plugin

Option A: Direct Install (Fastest)

/plugin install scientific-skills@claude-scientific-skills

Option B: Interactive Install

1. Run /plugin in Claude Code
2. Select Browse and install plugins
3. Choose claude-scientific-skills marketplace
4. Select scientific-skills
5. Click Install now

That's it! Claude will automatically use the appropriate skills when you describe your scientific tasks.

Managing Your Plugin:

# Check installed plugins
/plugin → Manage Plugins

# Update the plugin to the latest version
/plugin update scientific-skills@claude-scientific-skills

# Enable/disable the plugin
/plugin enable scientific-skills@claude-scientific-skills
/plugin disable scientific-skills@claude-scientific-skills

# Uninstall if needed
/plugin uninstall scientific-skills@claude-scientific-skills

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⌨️ Cursor IDE

One-click installation via our hosted MCP server:

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🔌 Any MCP Client (Not for Claude Code)

Access all skills via our MCP server in any MCP-compatible client (ChatGPT, Google ADK, OpenAI Agent SDK, etc.):

**Option 1: Hosted MCP Server