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 GUI	With Command Line
Work on the Google Cloud Platform	Link to the Google Cloud Platform Console Getting a trial account on the Google Cloud Platform sponsored by Google Getting a trial account on the Google Cloud Platform sponsored by ISB-CGC General information on how to use the Google Cloud Platform Console Specific information on how to set up your GCP project for use with ISB-CGC How to manage project members and change member permissions	Google Cloud SDK Google Cloud Shell Authenticating with Google (two approaches: gcloud init and/or gcloud auth login)
Explore what data are available	Documentation GUI	BigQuery R and Python Tutorials ISB-CGC Endpoints Google Genomics APIs
Understand details of the data	Access controlled data View File List in GUI View Sequences with IGV Google BigQuery Web UI Google API Explorer	For data in BigQuery BigQuery Command Line Tool BigQuery REST API For data in Google Cloud Storage Google Cloud Storage JSON API Google Cloud Storage gsutil For data in Google Genomics Google Genomics REST API
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	BigQuery R and Python Tutorials ISB-CGC Endpoints Google Genomics APIs
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 Google API Explorer before creating cohorts with command line tools	Use GUI saved cohorts in ISB-CGC Endpoints de novo using 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).	BigQuery R and Python Tutorials ISB-CGC Endpoints Google Genomics APIs
Run bioinformatics pipelines/tools		Google Compute Engine getting started guide Compute examples in Github (with Common Workflow Language (CWL) and grid examples) Useful recipes in the Google Genomics Cookbook
Import Genomic Data Commons lists		Introduction Importing GDC File Manifests Importing GDC Case lists

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