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
  • Cost Management
  • ISB-CGC Office Hours

USER GUIDE

  • Programs and Data Sets
  • ISB-CGC BigQuery Table Search
  • ISB-CGC BigQuery Tables
  • ISB-CGC Web Interface (Web App)
  • Cohort Builder/Data Explorer
  • Cancer Data File Browser
  • Mitelman Database
  • The TP53 Database
  • The Synthetic Lethality Resource
  • Human Tumor Atlas Network Data
  • Pipelines and APIs
  • Data Access and Security Overview
  • Accessing Controlled Data

MORE INFORMATION

  • ISB-CGC Notebooks
  • Statistical Notebooks
  • Machine Learning Notebooks
  • HTAN Notebooks
  • 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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