Reviewer response for version 1
The authors present regionReport, an R package to produce interactive HTML reports from a genomic-region based analysis, such as those produced by derfinder, bumphunter or DiffBind. 
The report shows quality control summaries, interactive tables of the most significant regions, and information on how regions lie in exons, introns, and intergenic regions. 
Both novice and expert genomicists are sure to gain much from this, and the paper clearly and concisely explains the software and its use, while providing useful examples and instructions.
The idea of producing common reports for a Bioconductor object is ingenious, and will hopefully inspire packages for other types of biological data. 
One of the great strengths of the package is the reproducibility practices it follows. 
For example, the section at the end of the produced report that shows reproducibility information, such as the original command, the session info, and the amount of time the report took to generate, is a great idea. 
(Indeed, the option to add sessionInfo() and timers could probably be baked into rmarkdown, or a thin wrapper thereof). 
Another strength is the use of modern knitr templates, such as expandable tables. 
Scientists who want to develop automated reports should use this package as a guide.
Overall my concerns are minor, and mostly concern the package rather than the paper, some of which I attempt to address in a GitHub pull request .
In pull request
- If the renderReport function leaves early (for example, if it is interrupted by the user hitting Stop) it strands the user's R session in a working directory. 
Using the on.exit function, as described here , lets R return to the original directory instead.
- The options for customization of the report are limited, by the customCode argument, to chunks between the main text and the reproducibility section. 
Genomicists may wish to take advantage of these reports while customizing some of their outputs. 
(For example, the authors of region-finding packages may wish to wrap renderReport with a customized template for their own objects). 
I've added a template argument in my pull request, and go over another suggestion below.
Not in pull request
- The `template` argument is a start towards greater customization, but a further improvement would be to allow the user to provide a list of customized internal chunks (for example, density-pvalue). 
As it is now, these are constructed in the renderReport function and cannot be altered without rewriting the entire function. 
This suggests finding a way to abstract them, such as bringing them in from a separate file, would be useful.
- As one example of an important customization I'd make: the reports show density plots of p-values and q-values, but in my experience genomicists are more accustomed to histograms (especially since bumps in density plots may be misleading, while histograms can get a better sense of which bumps are meaningful). 
I understand if the authors wish to keep it as a density plot, but if so I would appreciate a way to change it for my own use.
Minor issues
- The use of "smart quotes" in code within the PDF, such as source (“http://bioconductor.org/biocLite.R”), make it inconvenient to copy and paste them into an R terminal. 
If there's any way this could be remedied by the author or editors, it should.
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