This repository contains all of the analysis notebook required for the reproduction of the manuscript:
Analysis of matched tumor and normal profiles reveals common transcriptional and epigenetic signals shared across cancer types.
This code uses a number of features in the scientific python stack as well as a small set of standard R libraries. Thus far, this code has only been tested in a Linux enviroment, it may take some modification to run on other operating systems. I highly recomend installing a scientific Python distribution such as Anaconda or Enthought to handle the majority of the Python dependencies in this project (other than rPy2). These are both free for academic use.
pip install rpy2 These are Python packages that I use internally for things such as statistics and visualization. They are all available on my Github page, I recomend downloading them and installing them with python setup.py install. I appoligize for the generic names, I am hoping to develop these a bit more and make them into proper packages up to spec in my next code refactor.