This repository contains scripts built in-house for my Honours project.
Tree of files:\
honour-script/
├── DawnRank
│ ├── DawnRankAnalysis.main.R - main script for DawnRank analysis
│ └── dawnrank.visualisation.R - script for DawnRank visualisation
├── DriverNet
│ ├── DriverNetAnalysis.main.R - main script for DriverNet analysis
│ └── drivernet.visualisation.R - script for DriverNet visualisation
├── GSEA
│ └── gsea.analysis.R - Downstream analysis of GSEA results
├── general - scripts with functions used for more than one type of analysis
│ ├── PlottingFunctions.R - plotting heatmaps and barplots for driver gene prediction
│ ├── inf.graph.fix.R - checking and fixing influence graph (gene interaction network)
│ ├── influence.graph.R - building the initial influence graph (gene-gene interaction, which gene ID matching)
│ ├── influence.graph.ppi.R - building protein-protein interaction network (data from Dr Samuel Lee)
│ ├── influence.graph.ppi.and.ggi.R - combining ppi and ggi to get the gene interaction network
│ ├── mut.and.exp.matrix.R - patient data pre-processing to generate mutation and expression matrices
│ ├── parsePathways.R - parse the gene set file (.gmt) downloaded from MSigDB and helper functions
│ └── validation.mut.R - sample ID matching and analysis using the larger validation cohort (n = 190)
└── singscore
├── singscore.R - main script for singscore analysis
└── singscore.visualisation.R - visualisation of singscore results