Can I download RNA-seq and microarray data with this skill?

Yes, the skill includes specific implementations for downloading Series (GSE), Samples (GSM), and Platform (GPL) files for both array-based and sequence-based experiments.

What is the GEO Database skill for Claude Code?

It is a specialized capability that provides optimized Python patterns and scripts for accessing the NCBI Gene Expression Omnibus to retrieve and analyze functional genomics data.

Can I search for datasets based on specific diseases or organisms?

Yes, the skill provides advanced search patterns using MeSH terms and organism filters to precisely locate relevant datasets within the millions of samples in GEO.

How does this skill handle large file downloads?

The skill includes patterns for direct FTP access and asynchronous fetching to handle bulk data transfers and large supplementary files efficiently.

Does this skill require specific Python libraries?

It is designed to work with Biopython (Entrez) for searching and GEOparse for data handling, both of which are common in the bioinformatics ecosystem.

GEO Genomics Database Access

Name: GEO Genomics Database Access
Author: Microck

byMicrock

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データサイエンスとML

Simplifies searching, downloading, and analyzing gene expression datasets from the NCBI Gene Expression Omnibus (GEO) repository.

概要

This skill empowers researchers and bioinformaticians to programmatically interact with the NCBI GEO database. It provides standardized patterns for navigating the GEO hierarchy—including Series (GSE), Samples (GSM), Platforms (GPL), and DataSets (GDS)—and conducting advanced keyword searches via E-utilities. By leveraging tools like GEOparse and direct FTP access, it streamlines the complex process of data acquisition for transcriptomics and functional genomics, making it an essential utility for building automated bioinformatics pipelines and performing meta-analyses.

主な機能

Direct FTP access for bulk matrix and raw file downloads
Advanced metadata searching using NCBI Entrez E-utilities
81 GitHub stars
Navigate GEO data hierarchy including Series, Samples, and Platforms
Automated data retrieval and parsing with GEOparse integration
Standardized patterns for expression data filtering and preprocessing

ユースケース

Integrating public NCBI data into local computational biology workflows
Searching for specific gene expression profiles across thousands of public studies
Automating the retrieval of RNA-seq datasets for differential expression analysis

概要

主な機能

Direct FTP access for bulk matrix and raw file downloads
Advanced metadata searching using NCBI Entrez E-utilities
81 GitHub stars
Navigate GEO data hierarchy including Series, Samples, and Platforms
Automated data retrieval and parsing with GEOparse integration
Standardized patterns for expression data filtering and preprocessing

ユースケース

Integrating public NCBI data into local computational biology workflows
Searching for specific gene expression profiles across thousands of public studies
Automating the retrieval of RNA-seq datasets for differential expression analysis