This repository contains replication codes for the article about the gips R package.
The article is available HERE on arXiv.
The code is design to run under gips 1.2.1.
To run it, install the following packages (in this order):
install.packages("gips")
install.packages(c("ggplot2", "HSAUR2", "DAAG", "dplyr", "tidyr", "BiocManager",
"igraph", "gRim", "magrittr", "huge", "mvtnorm"))
BiocManager::install(c("GEOquery", "RBGL"))
install.packages("rags2ridges")
All folders are independent and produce plots to the plots folder. Inside the 3_(1|2|3)_* folders, the scripts are numbered in the order of running. If the code produces some output files, they are saved in this repository in the appropriate data folders. Time-consuming scripts have information in the first line on how long it took us to run.