Phd_thesis_exp

The repository contains the Jupyter Notebooks for my experiments in my PhD thesis and the source code for the methods I used to run.

• Title: Integrative Co-Expressed Gene Network Analysis for Bladder Cancer Subtyping Using Multi-Omics Data
• Supervisors: Dr A Mason, Dr D Halliday, Prof J Southgate, Prof S Smith
• Departments: School of Physics, Engineering and Technology & Department of Biology, University of York

Notebooks

Thre are three main folders for my notebooks each corresponding to a chapter in my thesis:

• clustering_analysis - chapter 3
• network_I - chapter 4 and 5
• network_II - chapter 6

The methods are described at length in my thesis which will be available on the white roses databases after the Viva and corrections.

Source code

• pgcna3.py - the modified version of the PGCNA work from Care et al. (2019). This is the script used to generate the networks in chapter 4
• iNet/ - represents the code for iNet and contains the network generated in chapter 6
• playground.py - how to run the iNet package
• NetworkAnalysis - suit of scripts used to analyse the networks generated

If any questions please don't hesitate to contact me