tcga-download-data
CommunityDownload TCGA data from GDC with merged matrices.
AuthorMDhewei
Version1.0.0
Installs0
System Documentation
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.
Dependency Matrix
Required Modules
requestspandasnumpy
Components
scripts
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: tcga-download-data Download link: https://github.com/MDhewei/bioinfor-claw/archive/main.zip#tcga-download-data Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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