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gtex-database

Retrieve RNA expression baselines and eQTL associations from the GTEx Portal API.

269|20|Updated Jun 13, 2026
Search Tags:#bioinformatics#genomics#gene expression#transcriptomics#eqtl#gtex
One-click install
npx skills add https://github.com/NeuroAIHub/BrainPilot --skill gtex-database-neuroaihub
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gtex-database
Source: https://github.com/NeuroAIHub/BrainPilot/tree/main/packages/skills/skills/09_Cellular_Molecular_Neuroscience/gtex-database
Command: npx skills add https://github.com/NeuroAIHub/BrainPilot --skill gtex-database-neuroaihub

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires polite-http, and includes scripts (resource) components.

What problem does it solve?

This skill solves the complexity of querying large-scale transcriptomics datasets by providing a streamlined interface to the GTEx Portal API, allowing researchers to retrieve baseline gene expression and eQTL data without manual API handling.

Core Features & Use Cases

  • Gene Expression Analysis: Retrieve median TPM values for genes across 54 non-diseased human tissue sites.
  • eQTL Discovery: Fetch significant expression Quantitative Trait Loci for specific genes or within defined chromosomal regions.
  • Use Case: A researcher investigating a candidate gene can use this skill to identify which tissues show the highest expression levels and whether genetic variants in that region correlate with expression changes in specific tissues.

Quick Start

Use the gtex-database skill to resolve the gene symbol TNF to its GENCODE ID and then fetch its median expression across all tissues.

Frequently Asked Questions about gtex-database

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

FAQPage Schema
How do I retrieve baseline gene expression data across human tissues from the GTEx portal?▼

To retrieve GTEx baseline gene expression, map your gene symbol to a GENCODE identifier and query the portal API for median TPM values across 54 non-diseased human tissue sites.

Can I fetch significant eQTL associations for a specific gene using the GTEx API?▼

Yes, you can fetch significant eQTL associations by querying the GTEx API for specific genes or within defined chromosomal regions to identify genetic variants correlating with tissue-specific expression changes.

Do I need the polite-http library to query GTEx transcriptomics data?▼

Yes, you need the polite-http library to ensure compliant, rate-limited interaction with GTEx API endpoints when querying transcriptomics datasets for RNA expression baselines and eQTL data.

What is the process for mapping a gene symbol like TNF to a GENCODE ID for GTEx queries?▼

To map a gene symbol like TNF to a GENCODE ID, use the skill to resolve the symbol before fetching its median expression across all tissues from the GTEx Portal API.

Are there limitations when querying large-scale transcriptomics datasets from the GTEx Portal?▼

The primary limitation is API rate limiting; queries to the GTEx Portal for RNA expression and eQTL data must be handled through compliant, rate-limited interactions using the polite-http library.

Does the gtex-database skill work for analyzing tissue-specific gene expression in genomic research?▼

Yes, the gtex-database skill facilitates genomic research by retrieving quantitative RNA expression baselines and significant eQTL associations, allowing you to identify which tissues show the highest expression levels.

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