Does this skill handle different GEO accession types?

Absolutely. It provides comprehensive support for Series (GSE), Samples (GSM), Platforms (GPL), and curated DataSets (GDS).

Do I need an NCBI API key to use these tools?

While an API key is not strictly required for low-volume requests, the skill recommends configuring your email with Entrez to comply with NCBI's usage policies for programmatic access.

Can I download raw sequence data using this skill?

Yes, the skill includes implementation patterns for downloading raw supplementary files and SRA data via FTP and Python-based automation.

What is the GEO Database skill for Claude Code?

It is a specialized capability that provides patterns and guidance for programmatically accessing, searching, and downloading gene expression data from the NCBI Gene Expression Omnibus.

Which Python libraries are used for GEO data retrieval?

The skill primarily utilizes GEOparse for downloading and parsing data, and Biopython (Entrez) for searching the NCBI databases.

GEO Database Access & Analysis

Name: GEO Database Access & Analysis
Author: plurigrid

byplurigrid

•

Ciencia de Datos y ML

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

The GEO Database skill empowers Claude to navigate and retrieve data from the NCBI Gene Expression Omnibus, the world's largest public repository for high-throughput gene expression data. It provides deep technical guidance on GEO's hierarchical data structures, including Series (GSE), Samples (GSM), and Platforms (GPL). By leveraging specialized Python libraries like GEOparse and Biopython, this skill enables researchers to automate the discovery of RNA-seq and microarray datasets, download expression matrices, and integrate public genomics data directly into computational analysis workflows.

Características Principales

018 GitHub stars

02Filtering and subsetting tools for gene-centric expression analysis

03Automated data parsing using GEOparse for Series Matrix and SOFT files

04Advanced NCBI E-utilities integration for complex metadata queries

05Direct FTP access patterns for downloading raw supplementary files

06Programmatic search and retrieval of GSE, GSM, and GPL accessions

Casos de Uso

01Automating the collection of experimental metadata for large-scale bioinformatics pipelines

02Downloading and preprocessing RNA-seq datasets for differential gene expression analysis

03Conducting meta-analyses across multiple GEO studies to identify robust biomarkers

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add plurigrid/asi geo-database

For use in Claude.ai and ChatGPT

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