geo-database

Search, download, and analyze GEO gene expression datasets in SOFT or Matrix formats.

1|Updated Jan 14, 2026

Search Tags:#analysis #bioinformatics #data retrieval #ncbi #geo #gene expression #transcriptomics

Ready to run

npx skills add https://github.com/Sologa/codex-pipeline --skill geo-database-sologa

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: geo-database
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/geo-database
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill geo-database-sologa

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires GEOparse, biopython, pandas, numpy, scipy, matplotlib, seaborn, statsmodels, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies the process of searching, downloading, and analyzing gene expression and genomics data from the NCBI Gene Expression Omnibus (GEO) database.

Core Features & Use Cases

Search & Retrieve: Find and download microarray and RNA-seq datasets (GSE, GSM, GPL) and their associated data files (SOFT, Matrix).
Data Analysis: Perform quality control, differential expression analysis, and correlation studies on downloaded datasets.
Use Case: A researcher needs to find all human breast cancer RNA-seq datasets submitted in the last year, download their expression matrices, and identify differentially expressed genes between control and treatment groups.

Quick Start

Use the geo-database skill to download the series matrix file for GSE123456.

Frequently Asked Questions about geo-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I download gene expression datasets from NCBI GEO?▼

You can download gene expression datasets from NCBI GEO by searching for GSE, GSM, or GPL records by keywords and retrieving their associated data in SOFT or Matrix formats via direct FTP access and E-utilities interaction.

Can I perform differential expression analysis on RNA-seq data retrieved from GEO?▼

Yes, you can perform differential expression analysis on RNA-seq data retrieved from GEO. The Skill supports downstream analysis including quality control, differential expression, and correlation studies using statsmodels and scipy.

Does this Skill support searching for GEO datasets by specific organisms and experimental conditions?▼

Yes, this Skill supports searching for GEO datasets by specific organisms and experimental conditions. You can filter microarray and RNA-seq records by keywords to find relevant genomics data for downstream retrieval.

Do I need Biopython and GEOparse to parse SOFT format files from GEO?▼

Yes, you need Biopython and GEOparse to parse SOFT format files from GEO. The Skill leverages these dependencies for programmatic data retrieval and manipulation of gene expression matrices.

What is the best way to analyze microarray data matrices downloaded from the GEO database?▼

The best way to analyze microarray data matrices downloaded from the GEO database is by using the integrated pandas, numpy, and seaborn libraries for data manipulation, statistical analysis, and visualization of gene expression patterns.

Why does my GEO data retrieval fail when downloading large series matrix files?▼

GEO data retrieval may fail when downloading large series matrix files due to FTP connection limits or E-utilities request caps. The Skill handles programmatic access, but large dataset downloads may require stable network connections and proper request pacing.