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.

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🧰 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.

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📄 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.

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🛠️ 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.

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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.

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↩️ Back to: Prepare & Upload Your Study