geo-database
NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.
npx skills add BioTender-max/awesome-bio-agent-skills --skill geo-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# GEO Gene Expression Omnibus Database ## Overview GEO (Gene Expression Omnibus) is NCBI's public repository for high-throughput functional genomics data, containing 200,000+ datasets (series) from microarrays, RNA-seq, ChIP-seq, methylation, and proteomics experiments. GEOparse provides a Python interface for downloading and parsing GEO records (GSE series, GPL platforms, GSM samples) while NCBI E-utilities enables programmatic search across GEO's metadata. ## When to Use - Searching for publicly available gene expression datasets by organism, tissue, disease, or experimental condition - Downloading and parsing a specific GEO series (GSE) with its expression matrix and sample metadata - Extracting sample annotation tables (e.g., treatment groups, clinical covariates) for meta-analysis - Loading microarray expression data (GPL platform-annotated probes) into a tidy DataFrame - Retrieving all GEO experiments associated with a gene or pathway of interest - Building automated pipelines that download and process GEO datasets for downstream analysis - For single-cell RNA-seq data at scale, use `cellxgene-census`; for aligned reads, download FASTQ from ENA/SRA instead ## Prerequisites -
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Query 1: Search GEO Datasets via E-utilities
- Query 2: Fetch Dataset Summary Metadata
- Query 3: Download and Parse a GEO Series
- Query 4: Extract Expression Matrix
- Query 5: Download Individual Sample (GSM)
- Query 6: Direct FTP Download for Large Series
- Key Concepts
- GEO Record Types
- SuperSeries and SubSeries
pip install GEOparse requests pandas
What does the geo-database skill do?
NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill geo-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.