This repository reproduces the R analyses from Tsakiroglou et al.
Packages used in the analyses can be installed by running install/install_r_libs.R in a fresh R session.
The package versions used for the manuscript analyses can be found within output/sessionInfo for each script.
Scripts to run the analyses from the manuscript can be found in code. Outputs from each analysis are already included in this repository, so each script can be run as a standalone analysis.
To reproduce the analysis from scratch using the data files in raw, each script should be run in the order they are numbered. Raw CEL files can be obtained from Gene Expression Omnibus (GEO) accession no. GSE276395 and should be saved in raw/GSE276395_RAW.