Does this skill require specific Python libraries?

Yes, it provides implementation patterns for the Biopython (Entrez) and GEOparse libraries, which are standard for interacting with NCBI databases programmatically.

What types of genomics data can this skill access?

This skill provides access to all major GEO data types, including Series (GSE) for full experiments, Samples (GSM) for individual replicates, Platforms (GPL) for technology annotations, and curated DataSets (GDS).

Can I download raw sequencing files using this skill?

Yes, the skill includes guidance for accessing supplementary files and using FTP protocols to download large-scale genomics data directly from NCBI servers.

Is an API key required for NCBI access?

NCBI Entrez requires a user email address to be provided with requests to identify the source and manage rate limits, which this skill helps you configure.

NCBI GEO Genomics Data Access

Name: NCBI GEO Genomics Data Access
Author: Yezez9

byYezez9

0•

データサイエンスとML

Accesses and integrates gene expression and functional genomics data from the NCBI Gene Expression Omnibus (GEO).

The geo-database skill empowers Claude to programmatically navigate the NCBI Gene Expression Omnibus, the world's largest public repository for high-throughput genomics data. It provides specialized implementation patterns for searching, retrieving, and parsing complex biological datasets including Series (GSE), Samples (GSM), and Platforms (GPL). By leveraging libraries like Biopython and GEOparse, this skill streamlines the transition from raw NCBI queries to structured dataframes, making it an essential tool for bioinformaticians and researchers conducting transcriptomics, RNA-seq, or microarray analysis.

主な機能

01Hierarchical data navigation for GSE, GSM, GPL, and GDS accessions

02Targeted gene expression profile querying across thousands of studies

03Direct FTP access patterns for bulk metadata and supplementary file downloads

04Programmatic search via NCBI E-utilities and Entrez API

05Automated dataset parsing and matrix extraction with GEOparse

060 GitHub stars

ユースケース

01Conducting meta-analyses by searching for specific phenotypes across multiple GEO series

02Integrating curated NCBI metadata into computational biology pipelines

03Automating the retrieval of RNA-seq datasets for differential expression workflows

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent geo-database

For use in Claude.ai and ChatGPT