The files for each study are also available from our datahub repository. This is basically the extracted version of the zip files in the Datasets Page. Note that this is a git LFS repo so if you are familiar with git you might prefer using this option.
API and API Clients
Besides downloading all the study data one can also request slices of the data using the API. A slice of the data could e.g. be "give me all the mutation data for one patient" or "get me all EGFR mutations for a particular group of samples". There are API clients available in a variety of languages including bash, R and Python. See for more information the API documentation.
Instance Maintainer Downloads
As an instance maintainer of cBioPortal there are a variety of files that might be helpful. See below.
Study staging files
Staging files for the studies on cbioportal.org can be download from the Datasets Page. These studies can be validated and loaded in a local cBioPortal instances using the validator and importer. Any issues with a downloaded study can be reported on cBioPortal DataHub.
TCGA Provisional studies often contain many different data types. These are excellent examples to use as reference when creating your own staging files. A detailed description on supported data types can be found in the File Formats documentation.
The seed database is a MySQL dump for seeding a new instance of the cBioPortal. Instructions for loading the seed database can be found here. The seed database for human can be downloaded from cBioPortal Datahub. A mouse version can be found here.