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Welcome to the ISB-CGC Community Notebook repository!

This repository holds notebooks that use Google cloud tools like BigQuery to illustrate common tasks in data analysis.

We try to design notebooks that are narrow in scope and answer a single question (like an FAQ).

A great (and easy!) way to try it out, is to jump over to https://colab.research.google.com, hit the 'github' tab in the dialog, and paste in https://github.com/isb-cgc/Community-Notebooks! The selected notebook will open in a free python environment. Please note that in many cases, you'll need a Google cloud project, such as for using BigQuery. But with a project, there is ample free compute available each month. For R notebooks, you'll probably want to open them in Rstudio.

To download this repository:

git clone https://github.com/isb-cgc/Community-Notebooks

Contents:

• Notebooks - contains both R and IPython notebooks.
• Common - helpful functions shared across notebooks.
• RegulomeExplorer - notebooks inspired by the TCGA http://explorer.cancerregulome.org/
• VM_Notebook_launcher - set of bash scripts to automate setup, and tear down, of VMs running jupyter.
• Beta - Drafts and Prototypes.

Documentation:

• ISB-CGC How Tos

Visit the WebApp: http://isb-cgc.org

Is something missing? Let us know in the issues, and please consider contributing a notebook!