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HowToGetStartedonISB-CGC.rst

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Quick-Start Guide

ISB-CGC provides both interactive (through a web application) and programmatic access to data hosted by institutes such as the Genomic Data Commons (GDC) and the Protemoic Data Commons (PDC) of the National Cancer Institute (NCI) and Human Tumor Atlas Network (HTAN), leveraging many aspects of the Google Cloud Platform. To get started, you'll need a Google Cloud Project.

Note that as of August 2024, ISB-CGC no longer supports controlled access data (including the IGV genomic viewer).

GettingStarted.png

Google Cloud Project Setup and Data Access

A Google Cloud Project (GCP) is required to make use of all of the data, tools, and Google Cloud functionality.

Obtain a Google identity

  • Do you or your institution already have a Google identity, such as a Gmail account? If so, you can proceed to the next step.
  • If not, it only takes a minute to create a Google identity. You can even link a non-Gmail account (eg. scientist@nih.gov) as a Google identity by this method.

Request Google Cloud Credits

  • Take advantage of a one-time $300 Google Credit.
  • If you have already used this one-time offer (or there is some other reason you cannot use it), see this information about how to request ISB-CGC Cloud Credits.

Set up a Google Cloud Project

Connect to ISB-CGC's cancer data tables in Google BigQuery

  • To obtain access to the ISB-CGC open access project tables in BigQuery, users can link these tables to their GCP project as described here.

Access open-access data

  • All individual processed data files are accessible through GDC Google Cloud Storage buckets; ISB-CGC provides pointers to these files. Examples of how to find these URLs are in this section, on each Program's documentation page; these SQL queries can also be incorporated into notebooks or workflows.

Getting Started with Analysis

Now you're ready to perform analysis. ISB-CGC offers web-based interactive interactive analysis, analysis with Google BigQuery and analysis using APIs and VMs. Please see the next section Getting Started with Analysis to learn more.