geo-database - Search and retrieve NCBI GEO genomics data
Search NCBI GEO for gene expression and functional genomics datasets, retrieve metadata and expression data, and download associated files.
Tags
Updated: 2026-10-19Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Search GEO datasets
- Search gene expression profiles
- Retrieve GEO metadata
- Download GEO datasets
- Parse GEO series
- Extract expression matrices
- Filter samples by metadata
- Fetch supplementary files
Inputs
- GEO search queries
- GEO accession identifiers
- Gene names
- Organism names
- Experimental conditions
- Download directories
- NCBI Entrez email
Outputs
- Search result records
- GEO metadata
- Expression matrices
- Downloaded GEO files
- Filtered sample subsets
- Expression profile records
Requirements
- Internet access
- Python environment
- GEOparse library
- Biopython library
- NCBI Entrez email