javier / examples-python

Analysis examples based on the ISB-CGC hosted TCGA data, using Python and IPython Notebooks.

examples-Python

This repository contains analysis examples based on the ISB-CGC hosted TCGA data in BigQuery, using Python, IPython Notebooks, and Google Cloud Datalab.

Where to start?

You can find an overview of the BigQuery tables in this notebook and from there, we suggest that you look at the two "Creating TCGA cohorts" notebooks (part 1 and part 2) which describe and make use of the Clinical and Biospecimen tables. From there you can delve into the various molecular data tables as well as the Annotations table. For now these sample notebooks are intentionally relatively simple and do not do any analysis that integrates data from multiple tables but once you have a grasp of how to use the data, developing your own more complex analyses should not be difficult. You could even contribute an example back to our github repository! You are also welcome to submit bug reports, comments, and feature-requests as github issues.

How to run the notebooks

1. Launch your own Cloud Datalab instance in the cloud or run it locally.
2. Work through the introductory notebooks that are pre-installed on Cloud Datalab.
3. Run git clone https://github.com/isb-cgc/examples-Python.git on your local file system to download the notebooks.
4. Import the ISB-CGC notebooks into your Cloud Datalab instance by navigating to the notebook list page and uploading them.

If you are running in the cloud, be sure to shut down Cloud Datalab when you are no longer using it. Shut down instructions and other tips are here.