Reviewer response for version 1
Needs more figures to demonstrate why a user would choose this tool. 
For example http://leekgroup.github.io/regionReportSupp/bumphunter-example/index.html (but even better would be to show an example, e.g. ITGB2 exon inclusion/exclusion or multiscale DMRs, where in our hands at least, nothing else short of IGV really does the job, and IGV doesn't do it that well.) 
The software is a firm foundation but the writeup needs work if it is to be compelling and thus influence readers to try out an unfamiliar tools.
My apologies for being harsh, but without figures, an applied paper simply will not be read. 
I would be less harsh if the underlying work were not compelling enough to command broader interest. 
A poor writeup will doom the work to obscurity.
Structure
Todo
Todo
Todo
Weakness
Other
Other