I have a single cell line where I have histone ChIP-Seq data for a control and data for the same cell line with treatment.
I then identified possible enhancer regions using the PARE program, and found that my control data came up with approximately 36k possible enhancer sites, while my treatment data came up with 34k.
I then ran bedtools to find sites that were similar between both sets.
I am now interested in finding quantitative differences between histone / TF signal at these enhancer sites. I ran a quick heatmap and metagene analysis and while they look how I expect them too, it isn't very easy to visually see this type of information. Is there a R package or a command line program that allows me to test whether one treated histone mark is more enriched in an enhancer site than my control treated histone mark?
Hopefully this makes sense. I'm still rather new to computational biology. Thank you.