Agent skill · research science · aiskillstore
geo-database
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
Why this skill is useful
Provides specific Python scripts for querying and retrieving gene expression datasets from the NCBI GEO database, which the AI wouldn't reliably generate on its own.
What it needs
Requires biopython installed locally. About 8k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
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. Core Capabilities 1. Understanding GEO Data Organization GEO organizes data hierarchically using different accession types: Series (GSE): A complete experiment with a set of related samples Example: GSE123456 Contains experimental design, samples, and overall study information Largest organizational unit in GEO Current count: 264,928+ series Sample (GSM): A single experimental sample or biological replicate Example: GSM987654 Contains individual sample data, protocols, and metadata Linked to platforms and series Current count: 8,068,632+ samples Platform (GPL): The microarray or sequencing platform used Example: GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array) Describes the technology and probe/feature annotations Shared across multiple experiments Current count: 27,739+ platforms DataSet (GDS): Curated collections with consistent formatting Example: GDS5678 Experimentally-comparable samples organized by study design Processed for differential analysis Subset of GEO data (4,348 curated datasets) Ideal for quick comparative analyses Profiles: Gene-specific expression data linked to sequence features Queryable by gene name or annotation Cross-references to Entrez Gene Enables gene-centric searches across all studies 2. Searching GEO Data GEO DataSets Search: Search for studies by keywords, organism, or experimental conditions: GEO Profiles Search: Find gene-specific expression patterns: Advanced Search Patterns: 3. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/geo-database--159d2f