Public cBioPortal

Cancer variant and gene expression visualizations.

✅

AACR Project GENIE cBioPortal

Project GENIE-only cancer variant and gene expression visualizations (includes many rare cancers)

🔒

AACR Project GENIE (cancer) raw data tables

Project GENIE-only cancer variant and gene expression row-level data tables (includes many rare cancers)

🔒

Catalog of Somatic Mutations in Cancer (COSMIC)

Common variants observed in cancer with functional annotation.

✅

Cancer Target Discovery and Development Data Portal

Wide variety of cancer drug discovery-related datasets.

✅

Open Pediatric Brain Tumor Atlas (OpenPBTA)

Various data types, including gene expression and somatic SNV data, for pediatric brain tumors (see: How to Obtain OpenPBTA Data and data file descriptions)

✅

Orphadata

Rare disease dataset repository managed by Orphanet.

✅ 🔒

Genomic Data Commons

Wide range of human cancer genomic data.

✅ 🔒

genomic and transcriptomic sequencing

Sequence Read Archive

Very wide range of human and non-human sequencing data.
Example searches: (noonan) AND "Homo sapiens"[orgn:__txid9606] or desmoid tumor

✅ 🔒

genomic and transcriptomic sequencing

refine.bio

Processed and harmonized microarray and RNA-seq datasets aggregated from public repositories. Friendly cohort building and download system. Example search

✅

transcriptomic sequencing

OpenNeuro

Neurology imaging datasets.

✅

imaging

GTEx

RNA-seq data from many different “normal” tissues, including skin and tibial nerve that may be useful as a point of comparison

✅ 🔒

genomic and transcriptomic sequencing