curatedTCGAData-mcp

What problem does it solve?

This Skill simplifies the complex process of accessing and preparing The Cancer Genome Atlas (TCGA) data for analysis, making multi-omic cancer research more accessible.

Core Features & Use Cases

• Discover Data: Easily list available cancer types and the specific data assays (e.g., RNA-seq, mutations, copy number) for each.
• Build Datasets: Create MultiAssayExperiment objects, which integrate various data types for a given cancer or multiple cancers.
• Data Filtering & Preparation: Filter data to include only primary tumors and extract essential clinical or subtype information.
• Use Case: A researcher wants to investigate gene expression differences between primary tumors and normal tissue for a specific cancer. They can use this Skill to find available RNA-seq data, build a dataset, filter for primary tumors, and extract the relevant expression matrix.

Quick Start

List all available TCGA cancer types.