Query NCBI GEO for public RNA-seq and microarray datasets by keyword, organism, or accession number.
npx skills add https://github.com/yf8578/clawomics --skill query-geo-yf8578
Please help me install this Agent Skill. Skill: query-geo Source: https://github.com/yf8578/clawomics/tree/main/skills/query-geo Command: npx skills add https://github.com/yf8578/clawomics --skill query-geo-yf8578
This Skill helps researchers quickly find publicly available gene expression datasets (RNA-seq, microarray) from the NCBI Gene Expression Omnibus (GEO) database, streamlining the process of data discovery for biological studies.
Use the query-geo skill to find RNA-seq datasets related to breast cancer in humans.
High-intent search queries and answers about installing and using this skill.
Search the NCBI GEO database by keywords, organism, or specific accession numbers to find public gene expression datasets. This retrieves RNA-seq and microarray dataset summaries, including titles, platforms, sample counts, and direct URLs.
Yes, you can search for RNA-seq datasets using specific GEO accession numbers like GSE or GDS. Querying these identifiers directly retrieves the corresponding dataset summaries, sample counts, platform details, and direct links to the GEO entries.
The GEO dataset summaries retrieved include titles, platform details, sample counts, and descriptive summaries of the studies. You also receive direct URLs linking to the original GEO entries for accessing the raw gene expression data.
You can locate microarray data for a specific organism in the GEO database by running a query filtered by organism name and relevant keywords. The search returns matching dataset summaries with sample counts and direct links to the GEO entries.
Yes, this GEO query tool works for both RNA-seq and microarray data. It queries the NCBI Gene Expression Omnibus database to find public gene expression datasets across both technologies, returning summaries and direct URLs for each.
The best way to find human breast cancer RNA-seq datasets on GEO is to query using combined keywords like breast cancer, human, and RNA-seq. This retrieves relevant dataset summaries, sample counts, platform details, and direct GEO entry URLs.
IDEA-XLSearch GEO databases for gene expression datasets by keywords and accession types.
ovachieverSearch GEO datasets and download gene expression data via E-utilities and GEOparse.
Imad-OuteQuery, download, and analyze NCBI GEO gene expression datasets with Python.
hxk622Search and download NCBI GEO microarray and RNA-seq datasets in SOFT and Matrix formats.
