Can I search for specific genes across different studies?

Yes, the skill includes patterns for searching GEO Profiles, which enables gene-centric searches to see expression patterns across various experimental conditions.

How does it handle large data downloads?

The skill provides implementation patterns for using GEOparse for automated downloads and direct FTP access via scripts for handling large supplementary files and matrices.

Does this skill require any external Python libraries?

Yes, it frequently utilizes GEOparse and Biopython (Entrez) to interact with NCBI servers and process data files.

Is an NCBI API key required?

While not strictly required for basic use, providing an email (and optionally an API key) for NCBI E-utilities is recommended and supported by the skill to avoid rate limiting.

What is the primary function of the GEO Database skill?

The skill allows Claude to help users search, download, and parse genomics data from the NCBI Gene Expression Omnibus, specifically handling Series (GSE), Samples (GSM), and Platforms (GPL).

NCBI GEO Genomics Assistant

Name: NCBI GEO Genomics Assistant
Author: K-Dense-AI

byK-Dense-AI

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3,719

데이터 과학 및 ML

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

소개

This skill provides Claude with the specialized ability to interact with the NCBI Gene Expression Omnibus (GEO) repository, a leading public database for high-throughput genomics data. It enables researchers and developers to programmatically search for microarray and RNA-seq datasets, retrieve complex metadata for Series (GSE) and Samples (GSM), and automate the download of expression matrices using tools like GEOparse and NCBI E-utilities. By streamlining the discovery and retrieval of biological data, this skill significantly reduces the overhead involved in setting up computational pipelines for differential gene expression and comparative genomics.

주요 기능

3,719 GitHub stars
Direct FTP download automation for SOFT and Matrix files
Programmatic data retrieval using the GEOparse Python library
Integration with NCBI E-utilities for high-performance metadata fetching
Gene-centric expression profile querying across multiple studies
Hierarchical search for GSE, GSM, GPL, and GDS accessions

사용 사례

Retrieving platform annotations to map probe IDs to genomic features
Locating RNA-seq datasets for specific organisms and disease conditions
Automating the download and parsing of expression matrices for meta-analysis

소개

주요 기능

3,719 GitHub stars
Direct FTP download automation for SOFT and Matrix files
Programmatic data retrieval using the GEOparse Python library
Integration with NCBI E-utilities for high-performance metadata fetching
Gene-centric expression profile querying across multiple studies
Hierarchical search for GSE, GSM, GPL, and GDS accessions

사용 사례

Retrieving platform annotations to map probe IDs to genomic features
Locating RNA-seq datasets for specific organisms and disease conditions
Automating the download and parsing of expression matrices for meta-analysis