This is an overview of the ISB Cancer Gateway (ISB-CGC) in the Cloud covering the use of the web app, BigQuery, and using the API.
How to Sign Up with a Google Account
This video will show you the steps necessary to sign up and link your google cloud project (GCP) to an ISB-CGC account. This enables you export to BigQuery tables and read and write to cloud buckets, including many other features.
How to Build a Cohort
In this video, we use the cohort builder to generate lists of cases (patients) based on various clinical and molecular features. Cohorts are saved and accessible as a list in the user's 'Saved Cohorts' panel (found in the Dashboard) and is the first step in any downstream analysis.
How to Make a Gene List
As a next step after building cohorts, we generate lists of clinical and molecular variables. These variables are connected to cohorts in the Workbooks, when analysis and plots are generated.
In this video we cover the new image viewers in the ISB-CGC web app. Starting with a cohort, we show how histology slides can be viewed using caMicroscope and how radiology images can be viewed using the Osimis DICOM viewer(note: now the OHIF viewer)
Learn how to export your cohorts in four different ways, including BigQuery, comma delimited files, cloud buckets and sharing with collaborators.