Getting Started with Analysis

ISB-CGC enables researchers to analyze cloud-based cancer data through a collection of powerful web-based tools and Google Cloud technologies. Learn more about the different analytical methods ISB-CGC users employ on their research projects.

Interactive web-based Cancer Data Analysis & Exploration

Explore and analyze ISB-CGC cancer data through a suite of graphical user interfaces (GUIs) that allow users to select and filter data from one or more public data sets (such as TCGA, CCLE, and TARGET), combine these with your own uploaded data and analyze using a variety of built-in visualization tools.

Cohort Builder/Data Explorer
Create and explore cohorts of interest
Interactive Pathology and Radiology Image Viewers
View images from cancer patients using integrated image viewers
Integrative Genomics Viewer (IGV)
Explore and visualize genomic data
Cancer Data File Browser
Browse and identify files associated with cohorts of interest
Mitelman Database for Chromosome Aberrations and Gene Fusions in Cancer
Explore relationships between chromosomal changes and cancer
The TP53 Database
Explore TP53 variant data that have been reported in the published literature or are available in other public databases.

Cancer data analysis using Google BigQuery

Processed data are consolidated by data type (ex. Clinical, DNA Methylation, RNAseq, Somatic Mutation, Protein Expression, etc.) from sources including the Genomics Data Commons (GDC) and Proteomics Data Commons (PDC) and transformed into ISB-CGC Google BigQuery tables. This allows users to quickly analyze information from thousands of patients in curated BigQuery tables using Structured Query Language (SQL). SQL can be used from the Google BigQuery Console but can also be embedded within Python, R and complex workflows, providing users with flexibility. The easy, yet cost effective, “burstability” of BigQuery allows you to, within minutes (as compared to days or weeks on a non-cloud based system), calculate statistical correlations across millions of combinations of data points.

BigQuery Table Search User Interface
Learn more about ISB-CGC hosted BigQuery tables
Google BigQuery Console
Use SQL to analyze and query ISB-CGC cancer data stored in Google’s cloud-based data warehouse
Seamlessly integrate ISB-CGC tables with R and Python to conduct robust analyses

Cancer data analysis using APIs & Google Cloud Virtual Machines

ISB-CGC enables the use of as many workflow technologies as possible through documentation, support, and necessary infrastructure.

Programmatically access data and user-generated cancer patient cohort information
Connecting to GA4GH and Cloud Life Sciences APIs:
Easily connect to APIs from ISB-CGC
Running workflows on ISB-CGC
Execute open-source and custom pipelines/algorithms on scalable virtual machines

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