scanpy

Want 10x the power with zero setup? [K-Dense Web](https://k-dense.ai) 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](https://k-dense.ai) | [Read our detailed comparison →](https://k-dense.ai/blog/k-dense-web-vs-claude-scientific-skills)

---

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.

---

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

---

• [What's Included](#whats-included)
• [Why Use This?](#why-use-this)
• [Getting Started](#getting-started)

- [Claude Code](#claude-code-recommended)

- [Cursor IDE](#cursor-ide)

- [Any MCP Client](#any-mcp-client-not-for-claude-code)

• [Support Open Source](#-support-the-open-source-community)
• [Prerequisites](#prerequisites)
• [Quick Examples](#quick-examples)
• [Use Cases](#use-cases)
• [Available Skills](#available-skills)
• [Contributing](#contributing)
• [Troubleshooting](#troubleshooting)
• [FAQ](#faq)
• [Support](#support)
• [Join Our Community](#join-our-community)
• [Citation](#citation)
• [License](#license)

---

⚡ **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

---

Choose your preferred platform to get started:

🖥️ Claude Code (Recommended)

> 📚 New to Claude Code? Check out the [Claude Code Quickstart Guide](https://docs.claude.com/en/docs/claude-code/quickstart) 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