Do I need an API key to use this skill?

While not strictly required for occasional queries, providing an email for NCBI Entrez/E-utilities is recommended to ensure higher rate limits and reliable data access.

What is the GEO Database skill for Claude?

It is a specialized capability that allows Claude to search, retrieve, and parse gene expression data from NCBI's public Gene Expression Omnibus repository.

Which biological data formats does this skill support?

The skill supports various formats including SOFT files, Series Matrix files, and MINiML through integration with the GEOparse library and FTP access.

How does this skill handle large genomic datasets?

It provides optimized patterns for batch processing via E-utilities and direct FTP download methods to handle large-scale data without exceeding memory limits.

Can I use this for both Microarray and RNA-seq data?

Yes, the skill is designed to handle both array-based and sequence-based functional genomics experiments stored in the GEO database.

NCBI GEO Data Access

Name: NCBI GEO Data Access
Author: K-Dense-AI

byK-Dense-AI

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2,188

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Data Science & ML

Accesses and manages NCBI Gene Expression Omnibus (GEO) data for transcriptomics and functional genomics research.

This skill enables Claude to programmatically interact with the NCBI Gene Expression Omnibus (GEO), the world's largest public repository for high-throughput gene expression data. It provides specialized capabilities for searching experimental series (GSE), individual samples (GSM), and platform metadata (GPL). By streamlining the use of specialized libraries like GEOparse and NCBI E-utilities, the skill facilitates complex bioinformatics workflows, including dataset retrieval, expression matrix extraction, and automated meta-analysis of RNA-seq and microarray data directly within the development environment.

Key Features

01Download and parse SOFT and Matrix files using GEOparse

022,188 GitHub stars

03Batch metadata retrieval via NCBI E-utilities

04Direct FTP access for large-scale genomic dataset downloads

05Query gene-specific expression patterns across studies

06Search GSE, GSM, and GPL accessions with complex queries

Use Cases

01Retrieving specific RNA-seq datasets for secondary analysis

02Automating experimental metadata collection for bioinformatics pipelines

03Searching for studies involving specific gene signatures or diseases

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills geo-database

For use in Claude.ai and ChatGPT

Download Skill