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.
Watch our introductory video guide to ISB-CGC
Or start with our intro notebook
To download this repository:
git clone https://github.com/isb-cgc/Community-NotebooksContents:
- Notebooks - contains both R and IPython notebooks.
- Common - helpful functions shared across notebooks.
- RegulomeExplorer - notebooks inspired by the TCGA http://explorer.cancerregulome.org/
- MitelmanDB - notebooks for processing data in the Mitelman database of chromosomal aberrations, including CytoConverter.
- MachineLearning - notebooks utilizing machine learning in BigQuery.
- SL-Cloud - the Synthetic Lethality Cloud notebook repository.
- HTAN - notebooks illustrating how to work with data of the Human Tumor Atlas Network https://humantumoratlas.org
- BQUserFunctions - a set of custom SQL functions for performing statistical tests in BigQuery.
- VM_Notebook_launcher - set of bash scripts to automate setup, and tear down, of VMs running jupyter.
- Retired - archive of deprecated notebooks
Documentation:
Visit the WebApp: http://isb-cgc.org
Is something missing? Let us know in the issues, and please consider contributing a notebook!