Frequently Asked Questions (FAQ)
ISB-CGC Accounts and Cloud Projects
I want to be able to run big jobs using Google Compute Engine on the TCGA data hosted by the ISB-CGC. What should I do?
You will need to request a Google Cloud Platform (GCP) project.
Can I use any email address as a Google identity?
Yes, you can. If your email address is not already linked to a Google account, you can create a Google account with your current email address. Please note, however that although these two accounts will then share the same name, they will still be two separate accounts, with two separate passwords, etc. (It is also possible that your institutional email address is already a Google account, if your institution uses Google Apps. This is how to find out).
How do I connect my Google Cloud Project to the ISB-CGC?
Your Google Cloud Project gives you access to all of the technologies that make up the Google Cloud Platform. These technologies include BigQuery, Cloud Storage, Compute Engine, etc. The ISB-CGC makes use of a variety of these technologies to provide access to the TCGA data, as well as many other data sets. Please see the Google Cloud Project Setup and Data Access section on the Getting Started with Analysis page.
The connection between your Google Cloud Project (whether it is an ISB-CGC sponsored and funded project or your own personal project) and the ISB-CGC is your Google identity (also referred to as your “user credentials”).
Access to all ISB-CGC hosted data is controlled using the Data Commons Framework Gen3 which defines the permissions attached to each data set, bucket, or object.
Data Access
Where can I find the TCGA data that ISB-CGC has made publicly available in BigQuery tables?
The BigQuery web interface can be accessed at https://console.cloud.google.com/bigquery. If you have not already added the ISB-CGC data sets to your BigQuery “view”, click on the blue arrow next to your project name at the top of the left side-bar, select “Switch to Project”, then “Display Project…”, and enter “isb-cgc-bq” (without quotes) in the text box labeled “Project ID”. For older ISB-CGC data sets, repeat and enter “isb-cgc”. All ISB-CGC public BigQuery data sets and tables will now be visible in the left side-bar of the BigQuery web interface. Note that in order to use BigQuery, you need to be a member of a Google Cloud Project.
Python Users
I want to write Python scripts that access the TCGA data hosted by the ISB-CGC. Do you have some examples that can get me started?
Yes, of course! The best place to start is with our Community Notebooks or our repository in GitHub. You can run any of these examples yourself. It includes an introduction explaining what Notebooks are, how to get started as a novice user, and how to run more advanced analyses once you are comfortable.
R Users
I want to use R and Bioconductor packages to work with the TCGA data. How can I do that?
You can run RStudio locally or deploy a dockerized version on a Google Compute Engine VM. You can find some great examples to get you started in our Community Notebooks or our repository in Community Notebooks GitHub.
For an example on how to use Bioconductor packages with TCGA data in BigQuery, please check out our interactive tutorial found here.
Regulome Explorer Users
Can I run Regulome Explorer Analyses using TCGA tables of heterogeneous data in BigQuery?
Yes, of course! A series of Python Notebooks have been created to replicate Regulome Explorer and includes detailed information on the statistical methods implemented. To get started, please visit our Regulome Explorer page in readthedocs or our Repository in Regulome Explorer GitHub.