NCBI GEO Database Explorer

About

This skill enables seamless integration with the NCBI Gene Expression Omnibus (GEO), the world's largest public repository for high-throughput genomics data. It provides specialized guidance for searching microarray and RNA-seq studies, downloading Series (GSE), Samples (GSM), and Platforms (GPL) data using industry-standard Python libraries like GEOparse and Biopython. Designed for bioinformaticians and researchers, it streamlines the complex process of fetching metadata, retrieving SOFT/Matrix files, and preprocessing large-scale biological datasets for transcriptomics and functional genomics analysis.

Key Features

• Pre-configured patterns for filtering and subsetting expression matrices
• Programmatic download and parsing of GSE/GSM/GPL records via GEOparse
• 16 GitHub stars
• Metadata retrieval and batch processing using NCBI E-utilities
• Search GEO DataSets and Profiles using complex keywords and organism filters
• Direct FTP access patterns for high-speed retrieval of Matrix and SOFT files

Use Cases

• Retrieving public RNA-seq datasets for comparative transcriptomics studies
• Searching for specific gene expression profiles across diverse disease states
• Automating the collection of microarray metadata for large-scale meta-analyses