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cBioPortal

The cBioPortal for Cancer Genomics provides visualization, analysis, and download of large-scale cancer genomics data sets. For a short intro on cBioPortal, see these introductory slides.

If you would like to know how to setup a private instance of the portal and/or get set up for developing, see the documentation. For details on contributing code changes via pull requests, see our Contributing document.

If you are interested in coordinating the development of new features, please contact cbioportal@cbioportal.org or reach out on https://slack.cbioportal.org.

📘 Documentation

See https://docs.cbioportal.org

  • The cBioPortal News page shows user focused release information (e.g. new data and new features)
  • The release notes on GitHub provide detailed information for each release for deployers/maintainers of cBioPortal
  • Docker Images are available for each tag and branch from Docker Hub

🐛 Bug Reports and Feature Requests

Please email us at cbioportal@googlegroups.com or file a ticket in the cbioportal/cbioportal isssue tracker.

📁 Repositories

Read the Architecture docs to see how these relate:

  • cbioportal: Backend
    • Read-only REST API written in Java Spring, which connects to MySQL database
    • Importer in Java Spring for loading data into MySQL database
    • Validator in Python for checking data file consistency with spec
  • cbioportal-frontend: Frontend in TypeScript/React
  • session-service: User Session Service in Java Spring
  • cbioportal-docker-compose: Recommended way to install cBioPortal and all its components using Docker
  • codebook: Analysis recipes for Python and R that leverage the cBioPortal REST API
  • datahub: Contains all public data files for published studies
  • datahub-study-curation-tools: Scripts to help curate studies for import into cBioPortal

📚 Cite

See How to Cite section of docs.

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  1. cbioportal cbioportal Public

    cBioPortal for Cancer Genomics

    Java 581 450

  2. codebook codebook Public

    A community shared resource of Python and R Notebooks that utilize the cBioPortal API for various analysis recipes

    Jupyter Notebook 9 11

  3. cbioportal-frontend cbioportal-frontend Public

    React Frontend of cBioPortal 🎉

    TypeScript 99 245

  4. datahub datahub Public

    A centralized location for storing curated data from cBioPortal

    HTML 166 118

  5. cbioportal-docker-compose cbioportal-docker-compose Public

    Run cBioPortal using Docker Compose

    Shell 12 28

  6. datahub-study-curation-tools datahub-study-curation-tools Public

    Contains tools used by cBioPortal data curators when preparing data for upload into the datahub repos.

    Python 16 13

Repositories

Showing 10 of 60 repositories