Datasets & Benchmarks

Curated cancer datasets and benchmarking resources.

TCGA Datasets

TCGA-BRCA

• Description: Breast Invasive Carcinoma
• Samples: 1,098 primary tumors
• Data Types: WGS, WXS, RNA-seq, miRNA, Methylation
• Download: GDC Portal

TCGA-LUAD

• Description: Lung Adenocarcinoma
• Samples: 1,185 primary tumors
• Data Types: WGS, WXS, RNA-seq, miRNA, Methylation
• Download: GDC Portal

TCGA-COAD

• Description: Colon Adenocarcinoma
• Samples: 521 primary tumors
• Data Types: WGS, WXS, RNA-seq, miRNA, Methylation
• Download: GDC Portal

Benchmark Datasets

MSK-IMPACT

• Description: Targeted sequencing panel
• Samples: 10,000+ patients
• Data Types: Targeted sequencing
• Download: cBioPortal

GENIE

• Description: AACR Project GENIE
• Samples: 100,000+ patients
• Data Types: Clinical + genomic
• Download: GENIE Portal

Single Cell Datasets

Human Cell Atlas

• Description: Single-cell reference atlas
• Samples: 1M+ cells
• Data Types: scRNA-seq, scATAC-seq
• Download: HCA Portal

Imaging Datasets

TCIA Collections

• Description: Medical imaging collections
• Samples: 100,000+ images
• Data Types: CT, MRI, PET, Pathology
• Download: TCIA Portal

Data Standards

• DICOM - Medical imaging
• BAM/SAM - Sequence alignment
• VCF - Variant calling
• MAF - Mutation annotation
• GFF/GTF - Genome annotation