skills/claude-scientific-skills
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Update skill counts and add TileDB-VCF to repository documentation

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- Update skill count badges and descriptions from 146 to 147 skills
- Add TileDB-VCF to genomic tools list in bioinformatics section
- Add variant database management use case for TileDB-VCF
- Add comprehensive TileDB-VCF entry to docs/scientific-skills.md
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Jeremy Leipzig
2026-02-24 12:07:21 -07:00
parent 730531e0d7
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README.md
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# Claude Scientific Skills
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE.md)
[![Skills](https://img.shields.io/badge/Skills-146-brightgreen.svg)](#whats-included)
[![Skills](https://img.shields.io/badge/Skills-147-brightgreen.svg)](#whats-included)
[![Agent Skills](https://img.shields.io/badge/Standard-Agent_Skills-blueviolet.svg)](https://agentskills.io/)
[![Works with](https://img.shields.io/badge/Works_with-Cursor_|_Claude_Code_|_Codex-blue.svg)](#getting-started)
A comprehensive collection of **146+ ready-to-use scientific and research skills** (now including financial/SEC research, U.S. Treasury fiscal data, OFR Hedge Fund Monitor, and Alpha Vantage market data) for any AI agent that supports the open [Agent Skills](https://agentskills.io/) standard, created by [K-Dense](https://k-dense.ai). Works with **Cursor, Claude Code, Codex, and more**. Transform your AI agent into a research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond.
A comprehensive collection of **147+ ready-to-use scientific and research skills** (now including financial/SEC research, U.S. Treasury fiscal data, OFR Hedge Fund Monitor, and Alpha Vantage market data) for any AI agent that supports the open [Agent Skills](https://agentskills.io/) standard, created by [K-Dense](https://k-dense.ai). Works with **Cursor, Claude Code, Codex, and more**. Transform your AI agent into a 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](https://k-dense.ai) for 200+ skills, cloud compute, and publication-ready outputs.
@@ -68,7 +68,7 @@ These skills enable your AI agent to seamlessly work with specialized scientific
## 📦 What's Included
This repository provides **146 scientific and research skills** organized into the following categories:
This repository provides **147 scientific and research skills** organized into the following categories:
- **30+ Scientific & Financial Databases** - Direct API access to OpenAlex, PubMed, bioRxiv, ChEMBL, UniProt, COSMIC, ClinicalTrials.gov, SEC EDGAR, U.S. Treasury Fiscal Data, Alpha Vantage, and more
- **55+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioPython, BioServices, PennyLane, Qiskit, and others
@@ -341,6 +341,7 @@ networks, and search GEO for similar patterns.
- **Sequence Analysis**: Process DNA/RNA/protein sequences with BioPython and pysam
- **Single-Cell Analysis**: Analyze 10X Genomics data with Scanpy, identify cell types, infer GRNs with Arboreto
- **Variant Annotation**: Annotate VCF files with Ensembl VEP, query ClinVar for pathogenicity
- **Variant Database Management**: Build scalable VCF databases with TileDB-VCF for incremental sample addition, efficient population-scale queries, and compressed storage of genomic variant data
- **Gene Discovery**: Query NCBI Gene, UniProt, and Ensembl for comprehensive gene information
- **Network Analysis**: Identify protein-protein interactions via STRING, map to pathways (KEGG, Reactome)
@@ -371,14 +372,14 @@ networks, and search GEO for similar patterns.
## 📚 Available Skills
This repository contains **143 scientific and research skills** organized across multiple domains. Each skill provides comprehensive documentation, code examples, and best practices for working with scientific libraries, databases, and tools.
This repository contains **144 scientific and research skills** organized across multiple domains. Each skill provides comprehensive documentation, code examples, and best practices for working with scientific libraries, databases, and tools.
### Skill Categories
#### 🧬 **Bioinformatics & Genomics** (16+ skills)
- Sequence analysis: BioPython, pysam, scikit-bio, BioServices
- Single-cell analysis: Scanpy, AnnData, scvi-tools, Arboreto, Cellxgene Census
- Genomic tools: gget, geniml, gtars, deepTools, FlowIO, Zarr
- Genomic tools: gget, geniml, gtars, deepTools, FlowIO, Zarr, TileDB-VCF
- Phylogenetics: ETE Toolkit
#### 🧪 **Cheminformatics & Drug Discovery** (11+ skills)