ISB Cancer Gateway in the Cloud
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GETTING STARTED

  • About the ISB-CGC Platform
  • ISB-CGC Data Overview
  • Quick-Start Guide
  • Getting Started with Analysis
  • How to Request Cloud Credits
  • Best Practices
  • Benefits of Using The Cloud

USER GUIDE

  • Programs and Data Sets
  • ISB-CGC Web Interface (Web App)
  • ISB-CGC BigQuery Tables
  • ISB-CGC BigQuery Table Search
  • Cancer Data File Browser
  • Mitelman Database
  • Cohort Builder/Data Explorer
  • Pipelines and APIs
  • ISB-CGC Notebooks
  • Statistical Notebooks
  • Data Access and Security Overview
  • Accessing Controlled Data

MORE INFORMATION

  • Tutorials and How-To Guides
  • Release Notes
  • Quick Links
  • Frequently Asked Questions (FAQ)
  • Contact Us
ISB Cancer Gateway in the Cloud
  • Docs »
  • Quick Links
  • Edit on GitHub

Quick LinksΒΆ

The table below describes the types of functions that can be performed in ISB-CGC and provides links to documentation on how to do those functions.

Function In web application With Command Line
Work on the Google Cloud Platform
  • Getting a trial account on the GCP sponsored by Google
  • Getting a trial account on the GCP sponsored by ISB-CGC
  • Specific information on how to set up your GCP project for use with ISB-CGC
  • Google Cloud SDK
  • Google Cloud Shell
  • Authenticating with Google
Understand details of the data
  • Access controlled data
  • View File List in GUI
  • View Sequences with IGV
  • Google BigQuery Walkthrough
  • Google BigQuery Console
  • For data in BigQuery
  • BigQuery Command Line Tool
  • Visualize results from BigQuery
  • For data in Google Cloud Storage
  • Google Cloud Storage JSON API
  • Google Cloud Storage gsutil
  • How to work with cloud storage notebook
Analyze ISB-CGC data
  • Analyses with Bar Charts, Histograms, Scatter Plots, Violin Plots, Cubby Hole Plots and SeqPeek
  • Google BigQuery Web UI and BigQuery UI Walkthrough
  • Community Notebooks
  • ISB-CGC Endpoints
Create cohorts of patients
  • Create cohorts
  • Cohorts set operations
  • Create a cohort from visualization (background and tool image)
  • Develop queries with Google BigQuery Web UI and/or ISB-CGC API v4 before creating cohorts with command line tools
  • Use GUI saved cohorts in ISB-CGC Endpoints
  • BigQuery Command Line Tool, and/or BigQuery REST API
Add your data to the cloud
  • Uploading your low level data (e.g. Bam and VCF files) to Google Cloud Storage
  • Upload high level summary data (such as Methylation, Gene Expression, microRNA, Protein Expression & Customized data) for plotting in the UI.
  • Uploading your data to Google Cloud Storage
  • Uploading your data to Google BigQuery
Analyze your data with ISB-CGC data
  • Plot your high level experimental data (such as Methylation, Gene Expression, microRNA, Protein Expression and Customized data) with other ISB-CGC data (e.g. TCGA).
  • Community Notebooks

Have feedback or corrections? Please email us at feedback@isb-cgc.org.
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