This repository contains data and code used in
Francesc Font-Clos, Stefano Zapperi, Caterina A. M. La Porta
Integrative analysis of pathway deregulation in obesity
npj Systems Biology and Applications (3) 18, 2017
link to journal
All the necessary datasets, including gene-expression data, pathway gene sets, and gene names dictionaries are stored in the data folder.
The main findings of the paper can be reproduced executing the following notebooks:
- SVDmerge to remove batch effects and merge gene-expression data
- Extracting the obesity signature
- The obesity score correlates with BMI
When executing the notebooks in order, several output files are generated. These include merged gene-expression data, the obesity signature and some figures. All output files are stored in the output folder
Please notice that you don't need to clone or install any of the dependencies if you just want to inspect the code and results of the manuscript. Github renders jupyter notebooks natively, so you can view all notebooks online.
If you want to run the code one your machine, the you must clone the repository locally and install all dependencies.
In addition to standard python packages such as numpy, pandas, matplotlib and seaborn, the code uses R's princurve package to compute PDS via rpy2.
Please contact Francesc Font-Clos for computational matters and Caterina A. M. La Porta for questions related to the manuscript's content.