Code for thesis "Construction and Analysis of Cancer Specific Interaction Networks by Co Expression"

This is the code used in my doctoral thesis "Construction and Analysis of Cancer-Specific Interaction Networks by Co-Expression Analysis in Colorectal Cancer" written by Piangfan Naksukpaiboon (Ph.D. in Medicine Queen's University Belfast, 2025).

Software or instrument-specific information needed to interpret the data: Majority of the dataset was processed using R and R studio. The code and packages associated to the code is currently compatible with R version 4.3.1 with exception of PMCMR and Netdist.

Main R packages used in this thesis include Tidygraph (version 1.2.0), tidyverse (version 1.3.1), ggplot2 (version 3.3.6), PMCMR (version 4.3), igraph (version 1.3.2), BEAM (version 2.0.2), Dplyr (version 1.0.9), data.table (version 1.14.2), org.Hs.eg.db (version 3.15.0), Netdist (version 0.4.9000), enrichR (version 3.1), survival (version 3.3-1), survminer (version 0.4.9), stringi (version 1.7.6), VennDiagram (version 1.7.3), textshape (version 1.7.3), readr (version 2.1.2), KEGGRest (version 3.1.5),
CMScaller (version 2.0.1) and pheatmap (version 1.0.12) (181).

The code is hosted in github. Please follow the link to access the information. Please note the link is private until a 1 year embargo period has lapsed. The embargo will lapse on 31 July 2026. Thereafter the code will be visible on github.