Based heavily on the main DESeq2 vignettes;
https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
Uses the RNA dataset generated from the paper;
"Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis"
http://doi.org/10.1016/j.xgen.2023.100306
Countdata is available from Zenodo and linked to in the script. For convienence a colData is supplied here from the supplementary table of the paper. As well as a file extracted from the GTF used for gene counts that links EMSEMBL ID with gene name.