In my experiment I compromise replication and transcription, then look into transcriptome for changes.
One thing that I would like to investigate is if the DEGs are significantly grouped in close-by loci through out genome or they are just scattered out in a random manner?
I would like to have your feedback on how to approach this question and which packages do you recommend?
I prefer to work under R environment if that's possible. The organism that I work on is S. pombe. Let me know if you need more information.
Thanks in advance,