README.md

This project provides an example of using ReactomeFIViz CyREST in a Python Jupyter notebook to perform a network comparison analysis between ovarian cancer and breast cancer using the TCGA mutation data sets.

Prerequisites

• Python version 2.6 or later.
• Python pandas package version 0.22.0 or later.
• The latest version of Cytoscape with the latest version of the ReactomeFIViz app.

Installation

• Install the required packages in a Python environment, e.g. in the Anaconda virtual environment:
  • conda create -n cytoscape pandas scipy statsmodels
  • source activate cytoscape
• Clone the example GitHub repository, e.g.:
  • mkdir ~/reactome-fi
  • cd ~/reactome-fi
  • git clone https://github.com/reactome-fi/workflows.git
  • cd workflows
  • The two TCGA MAF files were downloaded from the Broad Institute firehose server (http://gdac.broadinstitute.org) in April, 2018.
• In Cytoscape, select Help > Check for Updates to ensure that ReactomeFIViz is current.

Usage

• Start Cytoscape.

• In a console, start Jupyter on the notebook directory, e.g.:

  jupyter notebook --notebook-dir=~/reactome-fi/workflows
  

• Run all notebook cells in the web browser Jupyter window.