query-geo
Query NCBI GEO for gene expression datasets. Use when user asks about RNA-seq datasets, microarray data, expression data, GEO accessions, or finding public datasets. Triggers on "geo", "gene expression omnibus", "expression dataset", "RNA-seq dataset", "microarray dataset", "GSE", "GDS".
npx skills add BioTender-max/awesome-bio-agent-skills --skill query-geo --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.
# NCBI GEO Database Query Query Gene Expression Omnibus for public expression datasets. ## When to Use - User wants to find RNA-seq or microarray datasets - User asks about gene expression studies for a disease/tissue - User provides a GEO accession (GSE/GDS) to look up - User wants to download expression data ## How to Execute ```python from Bio import Entrez import json Entrez.email = "bioclaw@example.com" # 1. Search GEO datasets def search_geo(query, max_results=10, db="gds"): handle = Entrez.esearch(db=db, term=query, retmax=max_results, sort="relevance") record = Entrez.read(handle) handle.close() return record # 2. Get dataset summaries def geo_summary(id_list, db="gds"): ids = ",".join(str(i) for i in id_list) handle = Entrez.esummary(db=db, id=ids, retmode="json") result = json.loads(handle.read()) handle.close() return result # 3. Search for Series (GSE) def search_gse(keyword, organism="Homo sapiens", max_results=10): query = f'"{keyword}" AND "{organism}"[Organism] AND gse[ETYP]' return search_geo(query, max_results) # Example: Find breast cancer RNA-seq datasets search = search_gse("breast cancer RNA-seq", max_results=5) print(f"Found {search['Count']} datasets") if se
- When to Use
- How to Execute
- Search Syntax
- Follow-up Suggestions
What does the query-geo skill do?
Query NCBI GEO for gene expression datasets. Use when user asks about RNA-seq datasets, microarray data, expression data, GEO accessions, or finding public datasets. Triggers on "geo", "gene expression omnibus", "expression dataset", "RNA-seq dataset", "microarray dataset", "GSE", "GDS".
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill query-geo --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.