Preparing your files for upload to cBioPortal requires careful formatting and planning. This guide provides an overview of the process and links to examples, validation tools, and helper scripts.

🧰 Before You Begin

  • Create a folder to store your study files.
    The folder name must match the study ID given by the cBioPortal team. This ID must also appear in your meta files under cancer_study_identifier.

📝 Note: If you’d like to request a new or updated study ID, email the Data Governance team.

  • Once your files are nearly ready, validate them:
    1. Approved studies: Upload to the fh-dasl-cbio bucket. You’ll receive a validation report by email.
    2. Testing locally: Try running a local instance of cBioPortal and validate your study manually.

📄 Required and Optional Study Files

To be accepted for upload, your study must contain some required files. Others are optional but recommended depending on your dataset.

👉 Explore file format guide

📝 Note: Version 6 of cBioPortal requires at least one non-clinical file.

🛠️ Public Tools to Help Format Your Files

👉 Explore helper tools

These tools can help convert, validate, or format your data for cBioPortal. Choose the one that fits your data type and workflow best.

For more details, explore the full formatting documentation and helper tools here:

🔗 Full File Format Guide by cBioPortal

🔧 Overview of what a completed data “package” would look like for upload into cBioportal.

↩️ Back to: Prepare & Upload Your Study

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