Explore tumour histology and molecular data
TCGA provides a foundation for studying molecular variation across cancers alongside tissue morphology. This explorer brings together curated TCGA cohort definitions, molecular-data coverage and histology links, with selected spatial omics studies that add tissue and cellular context.
Explore available datasets, understand how measurements are linked, and assess their suitability for your research.
What we curated, and why
Building a research cohort requires more than finding available files. We review assay-quality annotations, treatment and diagnosis information, histological definitions and sample linkage. We document the resulting selections and uncertainties so that researchers can understand and adapt them.
Our current analysis panel was assembled for studies of tumour heterogeneity, including archetype analysis. Its selection criteria are explicit research choices; other questions may require different cohorts.
- Molecular coverageRNA-seq and 450k methylation by patient, counted separately and together.
- Assay and patient exclusionsQuality flags per aliquot, then treatment, diagnosis and specimen review per patient.
- Histology decisions and poolingHistology-defined cohorts, pooled projects and sensitivity subsets.
- Sample linkage and count unitsWhich images and measurements share a patient, sample or section, and what each count means.
Where to start
TCGA reference
TCGA cohorts, coverage and exclusionsCohort definitions, coverage by project, the analysis panel and patient-level data.Spatial studies
Matched H&E and spatial dataPublished studies that pair H&E images with spatial measurements, and what has been verified for each.Curation and methods
How selections were madeExclusions, histology decisions, pooling, linkage, count units and limitations.Research applications
What the data can supportFrom tumour heterogeneity and classification to histology-to-molecular modelling and archetypes.Ready for AI agents
Everything on this site is also published as text and JSON for AI assistants and scripts. A read-only MCP server lets assistants such as Claude query the catalogue directly, with counts defined as on these pages.
MCP server
Query the catalogue from ClaudeTen read-only tools for resources, tissue sections and TCGA patients. Runs on your computer.llms.txt
Agent guideWhat the site is, what to read before using any count, and links to every text version.Text and JSON
Pages and data for scriptsMarkdown pages, one JSON file per cancer type, a checksummed data index, schemas and a glossary.AGENTS.md
For coding agentsCommands, generated files and rules for agents working on the repository.Browse by cancer type
Each cancer page shows the TCGA data and the spatial studies available for that cancer, with the checks that remain open. The list follows the current analysis panel: colorectal cancer and diffuse glioma also have pooled pages.
Kinds of data
| Layer | What it contains | Typical use | Entries |
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