The Gene Expression Omnibus (GEO) is a public repository for high-throughput gene expression and functional genomics data hosted by the National Center for Biotechnology Information (NCBI).

How do I download a specific dataset using this skill?

You can use the GEOparse library patterns within the skill to call get_GEO(geo='GSEXXXXXX'), which automatically retrieves and parses both metadata and expression matrices.

Does this skill support both microarray and RNA-seq data?

Yes, it supports searching and retrieving data for both array-based and sequence-based experiments, including access to Series (GSE) and Samples (GSM).

Can I filter GEO searches by specific conditions?

Yes, the skill provides advanced search patterns using NCBI E-utilities to filter by organism, publication date, author, technology type, and MeSH terms.

GEO Database Access

Name: GEO Database Access
Author: pur3v4d3r

bypur3v4d3r

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データサイエンスとML

Integrates with the NCBI Gene Expression Omnibus (GEO) to search, download, and analyze high-throughput functional genomics datasets.

概要

The GEO Database skill empowers researchers and developers to programmatically access NCBI's vast repository of transcriptomics and genomics data directly within Claude. It provides specialized patterns for querying series (GSE), samples (GSM), and platforms (GPL), and automates the retrieval of SOFT and Matrix files using libraries like GEOparse and Bio.Entrez. This skill is essential for bioinformatics workflows, facilitating the meta-analysis of gene expression and the integration of public biological data into computational pipelines with ease.

主な機能

Automated parsing of series matrix and SOFT files with GEOparse integration
Batch downloading of supplementary files and raw sequencing data from NCBI FTP servers
Pre-configured patterns for integrating GEO data into Python bioinformatics stacks
1 GitHub stars
Advanced search for GSE, GSM, and GPL accessions using MeSH terms and filters
Programmatic metadata extraction for experimental design and sample characteristics

ユースケース

Extracting transcriptomics data for differential gene expression meta-analysis
Retrieving specific platform annotations (GPL) to map probes to gene symbols
Automating the search for public RNA-seq datasets related to specific diseases or organisms

概要

主な機能

Automated parsing of series matrix and SOFT files with GEOparse integration
Batch downloading of supplementary files and raw sequencing data from NCBI FTP servers
Pre-configured patterns for integrating GEO data into Python bioinformatics stacks
1 GitHub stars
Advanced search for GSE, GSM, and GPL accessions using MeSH terms and filters
Programmatic metadata extraction for experimental design and sample characteristics

ユースケース

Extracting transcriptomics data for differential gene expression meta-analysis
Retrieving specific platform annotations (GPL) to map probes to gene symbols
Automating the search for public RNA-seq datasets related to specific diseases or organisms