How does it handle large expression matrices?

The skill utilizes the GEOparse library and Pandas to efficiently download, pivot, and load series matrix files for high-performance computational analysis.

What accession types are supported by the GEO skill?

The skill supports all major GEO accession types including Series (GSE), Samples (GSM), Platforms (GPL), and DataSets (GDS).

Do I need an API key to access NCBI data?

While a specific API key is not required, the skill utilizes Biopython's Entrez which requires a valid email address to identify your requests to NCBI servers.

Is it possible to search for specific genes across studies?

Yes, the skill includes specialized search patterns for querying GEO Profiles by gene name, organism, and experimental conditions.

Can this skill download raw sequence data?

Yes, the skill provides patterns for accessing supplementary files and metadata that can be used to locate and download SRA files for raw sequencing analysis.

NCBI GEO Genomics Database

Name: NCBI GEO Genomics Database
Author: Microck

byMicrock

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Data Science & ML

Accesses and analyzes gene expression and functional genomics data from the NCBI Gene Expression Omnibus repository.

The NCBI GEO Skill provides a comprehensive toolkit for bioinformaticians and researchers to programmatically search, retrieve, and analyze high-throughput genomics data. It streamlines the workflow for accessing over 264,000 studies including microarrays and RNA-seq datasets via GSE, GSM, and GPL accessions. By integrating Python libraries like Biopython and GEOparse, this skill enables seamless downloading of SOFT or Matrix files, metadata extraction, and preparation for downstream transcriptomics analysis directly within the Claude environment, making it ideal for researchers automating their biological data pipelines.

Key Features

01Comprehensive search across GSE, GSM, and GPL accession types

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03Metadata extraction for experimental design and sample characteristics

04Advanced querying for specific organisms, platforms, or gene profiles

05Direct FTP access for downloading raw and processed matrix files

06Automated data retrieval using GEOparse and Biopython Entrez

Use Cases

01Analyzing gene expression patterns across different disease states or tissues

02Fetching RNA-seq datasets for comparative transcriptomics studies

03Building automated bioinformatics pipelines for high-throughput data collection

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills geo-database

For use in Claude.ai and ChatGPT

Download Skill