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MDhewei
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gtex-download-data

Download GTEx expression data matrices from the GTEx Portal API or static files.

64|12|Updated Apr 7, 2026
Search Tags:#matrices#expression#download#rna-seq#gtex#tissues
One-click install
npx skills add https://github.com/MDhewei/bioinfor-claw --skill gtex-download-data
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gtex-download-data
Source: https://github.com/MDhewei/bioinfor-claw/tree/main/public-datasets-access-and-download/gtex-download-data
Command: npx skills add https://github.com/MDhewei/bioinfor-claw --skill gtex-download-data

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, numpy, and includes scripts (resource) components.

What problem does it solve?

GTEx data is dispersed across portals; this Skill centralizes acquisition of gene expression data (bulk RNA-seq TPMs, read counts, or median expression) into ready-to-analyze tissue×gene matrices.

Core Features & Use Cases

  • Retrieve median TPM, sample TPM, read counts, tissue metadata, or gene-specific TPM across tissues.
  • Filter by tissues and/or genes and save filtered matrices for downstream analyses.
  • Use with or without an optional manifest to track provenance for reproducibility.

Quick Start

Run the GTEx data downloader to fetch median TPM, sample TPM, read counts, or tissue metadata for specified tissues and genes, saving results to TSV.

Frequently Asked Questions about gtex-download-data

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

FAQPage Schema
How do I download GTEx RNA-seq expression data across specific tissues and genes?▼

You can download GTEx bulk RNA-seq TPMs and read counts by fetching data matrices from the GTEx Portal API, applying optional tissue and gene filters, and saving the resulting tissue×gene matrices to TSV files.

What GTEx data types are available for building tissue-gene matrices?▼

You can retrieve median_tpm, sample_tpm, read_counts, tissue_metadata, and gene_tpm data types to construct tissue×gene matrices for downstream analyses and data integration.

Can I use pandas to filter GTEx expression matrices by specific tissues?▼

Yes, you can use pandas alongside the skill's optional tissue and gene filtering parameters to subset GTEx expression matrices, yielding filtered tissue×gene outputs ready for downstream analysis.

Does the GTEx data downloader support both v8 and v10 datasets?▼

The downloader supports both GTEx v8 and v10 datasets, enabling you to fetch version-specific bulk RNA-seq TPMs, read counts, and tissue metadata for reproducible downstream integration.

How do I track provenance when downloading GTEx read counts and TPM matrices?▼

You can track provenance by enabling the optional manifest output, which records metadata about the downloaded GTEx expression matrices to ensure reproducibility for downstream analyses.

What's the best way to get GTEx median TPM data into a ready-to-analyze matrix format?▼

The best way is to use a centralized downloader that queries the GTEx Portal API or static files, retrieves median TPM data, and outputs ready-to-analyze tissue×gene matrices in TSV format.

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