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Welcome to the wiki pages for WEHI's cBioPortal instance!
This wiki contains documentation regarding the setup and use of the cBioPortal instance hosted by WEHI.
See the setup page for how to setup the instance again.
If you want to prepare your mutation data for import into cBioPortal, follow the rough guidelines on cBioPortal's datahub repo.
An experimental pipeline is now available to convert and annotate VCFs into MAFs for import into cBioPortal. See our repository and relevant wiki page.
The backend database has been migrated to use both the hg19 (GRCh37) and hg38 (GRCh38) reference genomes. Combining studies that use different reference genomes will give you a warning. While reference genomes are highly concordant, ensure to check the results. New studies have also been updated to match the Datahub repository at 31db862.
Token authentication has been enabled, meaning you can query the WEHI instance of cbioportal using cBioPortalR. To get a token, click on "Logged in as [email protected]", click on "Data Access Token", and click "Download Token". Follow the Installation and Authenticaiton instructions to get started. When using cBioPortalR, connect to the WEHI cBioPortal instance with set_cbioportal_db(db="cbioportal-test.wehi.edu.au").
The instance has been opened up to all WEHI staff! Anybody within the WEHI network should be able to login using their WEHI credentials.
Two BCRL test datasets have been added: Anheart Pilot Methylation, and FFPE vs SNAP Optimisation methylation. These are only visible to users with the BCRL group applied.
Integration with WEHI's authentication has been setup, meaning you can login with your WEHI credentials. If you have trouble logging in, send an email to [email protected].
We've got our cBioPortal instance going! Thanks to Tim from ITS for setting this up. Currently working on:
- Adding gene panels and public datasets from datahub
- Figuring out why a few gene panels and public datasets cannot be added properly
- Setting up authentication