Quick Links

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

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