Geo Database

This connects you to NCBI's Gene Expression Omnibus, the public repository with 264,000+ genomics studies and 8 million samples. You get programmatic access through GEOparse and E-utilities to search for microarray and RNA-seq datasets, pull down expression matrices, and grab supplementary files. The hierarchical structure (GSE series, GSM samples, GPL platforms) takes a minute to internalize, but once you do, it's straightforward to filter by organism or condition, extract gene-specific profiles, or build comparative analyses. Handles both the curated GDS collections and raw experimental data. If you're doing transcriptomics work and need existing datasets for validation or meta-analysis, this saves you from manual downloads.

skills.sh installs: 350
GitHub stars: 33.2K
last updated: Aug 21, 2026

View on GitHub

Install

$ npx -y skills add davila7/claude-code-templates --skill geo-database --agent claude-code

Installs into .claude/skills of the current project.

Files

GEO Database

Overview

The Gene Expression Omnibus (GEO) is NCBI's public repository for high-throughput gene expression and functional genomics data. GEO contains over 264,000 studies with more than 8 million samples from both array-based and sequence-based experiments.

When to Use This Skill

This skill should be used when searching for gene expression datasets, retrieving experimental data, downloading raw and processed files, querying expression profiles, or integrating GEO data into computational analysis workflows.