bio-geo-data - Query NCBI GEO datasets using Biopython Bio.Entrez.
Query NCBI Gene Expression Omnibus for expression datasets using Biopython, get download links, and link GEO series to SRA runs.
Tags
Updated: 2026-09-22Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Search GEO datasets
- Fetch GEO dataset summaries
- Retrieve FTP download links
- Link GEO series to SRA
- Link PubMed IDs to GEO
- Download series matrix files
Inputs
- NCBI Entrez email and API key
- GEO search queries or accessions
- PubMed IDs
Outputs
- GEO search summaries
- FTP download URLs
- Associated SRA run IDs
- Downloaded series matrix files
Requirements
- Python environment
- Biopython library
- GEOparse library
- NCBI Entrez API access