tcga-download-data

Download TCGA genomic datasets from the GDC Data Portal with streaming and MD5 verification.

64|12|Updated Apr 7, 2026

Search Tags:#merge #expression #download #mutations #clinical #tcga #gdc

Ready to run

npx skills add https://github.com/MDhewei/bioinfor-claw --skill tcga-download-data

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: tcga-download-data
Source: https://github.com/MDhewei/bioinfor-claw/tree/main/public-datasets-access-and-download/tcga-download-data
Command: npx skills add https://github.com/MDhewei/bioinfor-claw --skill tcga-download-data

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the retrieval of TCGA genomic datasets from the GDC Data Portal, enabling users to download expression, mutations, CNV, clinical data, and methylation data, while producing per-file manifests and merged matrices for downstream analysis.

Core Features & Use Cases

Download datasets by data type and cancer type from the GDC API with streaming downloads and integrity checks.
Merge related files into gene × sample expression matrices, combined mutation records, and CNV matrices; generate a provenance manifest for reproducibility.
Use in pipelines to prepare data for downstream genomic analyses, comparative studies, or publication-ready results.

Quick Start

Query the GDC for the requested cancer type and data type, download the raw files to your output directory, and generate merged matrices for immediate analysis.

Frequently Asked Questions about tcga-download-data

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

FAQPage Schema

How do I download TCGA data from GDC and merge it into an expression matrix?▼

Download TCGA data from GDC by querying the API for specific cancer and data types, streaming raw files to a directory, and merging related files into gene × sample expression matrices with a provenance manifest.

What's the best way to automate TCGA clinical and mutation data retrieval from the GDC Data Portal?▼

Automate TCGA clinical and mutation data retrieval from the GDC Data Portal by querying the API, streaming downloads, and merging related files into combined records and matrices with retry logic and error handling.

Does the TCGA download process include file integrity verification?▼

Yes, the TCGA download process includes MD5 verification and retry logic to support reliable data acquisition and ensure raw file integrity during streaming downloads from GDC.

Can I query GDC for specific cancer types when downloading TCGA datasets?▼

Yes, you can query the GDC API by cancer type and data type to download specific TCGA genomic datasets, including expression, mutations, CNV, clinical, and methylation data.

What dependencies do I need to download TCGA data and generate merged matrices?▼

You need the requests, pandas, and numpy dependencies to download TCGA data, manage directory structures, and merge related files into matrices for downstream analysis.

Why does my TCGA data download fail when pulling large genomic datasets from GDC?▼

TCGA data downloads from GDC may fail due to network interruptions, but the process includes retry logic and robust error handling to manage streaming failures and ensure reliable data acquisition.