Do I need an account to use the GEO database features?

While public data is accessible without an account, providing an email for NCBI Entrez or using an NCBI API key is recommended to avoid rate limiting and ensure stable data retrieval.

Does this skill support automated data parsing?

Yes, it provides implementation patterns for using the GEOparse library and Biopython's Entrez module to programmatically parse metadata and expression matrices into Python-ready formats like Pandas DataFrames.

What types of genomic data can I access with this skill?

You can access all data hosted in the NCBI GEO repository, including microarray experiments, RNA-seq, ChIP-seq, and various other high-throughput functional genomics studies.

Can I download raw supplementary files like FASTQ or SRA?

The skill includes methods for navigating GEO's FTP structure, allowing you to programmatically locate and download raw or processed supplementary files for any study.

NCBI GEO Scientific Data Access

Name: NCBI GEO Scientific Data Access
Author: jimmc414

byjimmc414

•

324

•

데이터 과학 및 ML

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

The geo-database skill empowers Claude to act as a bioinformatics assistant by providing specialized patterns for interfacing with the NCBI Gene Expression Omnibus repository. It enables the discovery and retrieval of high-throughput experimental data, including RNA-seq, microarrays, and other functional genomics datasets. By utilizing industry-standard tools like GEOparse and Entrez E-utilities, the skill facilitates the transition from biological query to processed expression matrix, making it indispensable for researchers performing meta-analyses, cross-study comparisons, or automated data mining in the life sciences.

주요 기능

01Hierarchical search across GEO Series (GSE), Samples (GSM), and Platforms (GPL).

02Automated extraction of expression profiles and experimental metadata.

03Advanced query building via NCBI E-utilities for specific organisms, tissues, or diseases.

04Direct FTP access patterns for downloading large-scale supplementary data and raw files.

05324 GitHub stars

06Programmatic data retrieval using GEOparse for automated matrix and SOFT file handling.

사용 사례

01Identifying relevant RNA-seq datasets for specific diseases or experimental conditions.

02Extracting gene-specific expression patterns across thousands of publicly available samples.

03Automating the download and preprocessing of transcriptomics studies for downstream meta-analysis.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jimmc414/kosmos geo-database

For use in Claude.ai and ChatGPT

Download Skill