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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Ciencia de Datos y ML

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

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.

Características Principales

01Automated parsing of series matrix and SOFT files with GEOparse integration

02Batch downloading of supplementary files and raw sequencing data from NCBI FTP servers

03Pre-configured patterns for integrating GEO data into Python bioinformatics stacks

041 GitHub stars

05Advanced search for GSE, GSM, and GPL accessions using MeSH terms and filters

06Programmatic metadata extraction for experimental design and sample characteristics

Casos de Uso

01Extracting transcriptomics data for differential gene expression meta-analysis

02Retrieving specific platform annotations (GPL) to map probes to gene symbols

03Automating the search for public RNA-seq datasets related to specific diseases or organisms

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add pur3v4d3r/pur3-pkb-codebase geo-database

For use in Claude.ai and ChatGPT

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