scientific-geo-expression

Search GEO datasets and retrieve expression matrices for transcriptomics analyses.

3|1|Updated Feb 11, 2026

Search Tags:#expression #microarray #differential-expression #geo #rna-seq #gse #gds

Ready to run

npx skills add https://github.com/nahisaho/satori --skill scientific-geo-expression

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: scientific-geo-expression
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-geo-expression
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-geo-expression

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Automates discovery and retrieval of GEO datasets and expression matrices to accelerate transcriptomics analyses.

Core Features & Use Cases

GEO dataset search (GDS/GSE) and metadata extraction
Expression matrix download for downstream analyses (DEG, clustering)
Cross-dataset comparisons and metadata-driven filtering for reproducible workflows

Quick Start

Query GEO data and fetch the corresponding expression matrix for a chosen study.

Frequently Asked Questions about scientific-geo-expression

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

FAQPage Schema

How do I download GEO expression matrices for differential expression analysis?▼

You can search GEO datasets (GSE or GDS) by query, organism, and study type, then retrieve the corresponding expression matrices and metadata CSVs to support downstream differential expression analysis.

Can I search GEO datasets by organism and study type?▼

Yes, you can search GEO datasets by specifying inputs such as organism and study type, allowing you to apply metadata-driven filtering to find relevant transcriptomics data.

What is the best way to extract RNA-seq data from GEO for cross-dataset comparisons?▼

The best way to extract RNA-seq data for cross-dataset comparisons is to query GEO datasets and retrieve expression matrices, applying metadata-driven filtering to align studies and support reproducible analyses.

Does this Skill support both GDS and GSE dataset formats?▼

Yes, the Skill supports both GDS and GSE dataset formats, allowing you to search and extract expression data across both GEO dataset types for transcriptomics analyses.

How do I handle failures when retrieving microarray expression data from GEO?▼

The Skill includes failure handling to support end-to-end GEO workflows, managing issues that arise when retrieving microarray expression data to ensure reproducible transcriptomics analyses.

What outputs do I get when querying GEO datasets for transcriptomics analysis?▼

When querying GEO datasets, the outputs include expression matrices and metadata CSVs, which provide the necessary data for downstream differential expression, clustering, and cross-dataset comparisons.