alterlab-geo
Installation
SKILL.md
GEO Database
Overview
The Gene Expression Omnibus (GEO) is NCBI's public repository for high-throughput gene expression and functional genomics data. It holds hundreds of thousands of studies (Series) and millions of samples from both array-based and sequence-based experiments. For current totals see the GEO browser at https://www.ncbi.nlm.nih.gov/geo/.
When to Use This Skill
Use this skill 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.
Does NOT Trigger
| Scenario | Use Instead |
|---|---|
| Raw FASTQ reads by SRA/ENA run accession | alterlab-ena |
| Reference normal-tissue expression (median TPM, eQTLs) | alterlab-gtex |
| Harmonized single-cell expression across studies (CELLxGENE Census) | alterlab-cellxgene |
| Running differential expression on a count matrix you already have | alterlab-pydeseq2 |
| Tumor mutations / copy number in cancer cohorts | alterlab-cbioportal |