igor

Thanks for clarifying. I guess we at least know where the problem is. Maybe the solution could be to just add an if-else based on `signaldist.analStd()` output? Not very elegant,...

By if-else, I meant if `signaldist.analStd()` returns `nan`, then you could fall back to the slow method. Obviously you would know all the possible caveats better than me, so I...

Unfortunately, I am running this on a cluster and can't use Docker. Obviously it would be nice to have a Docker image for people who can use that option.

Thanks for the suggestion @vatese ! I was also on CentOS 6 with gcc 4.4. I switched to gcc 6.1. Everything seems to be working now. `test.occpeaks.bed.gz` is 160 lines...

Thank you for your interest. The gene conversion happen using a different package `babelgene`. The [vignette](https://cran.r-project.org/web/packages/babelgene/vignettes/babelgene-intro.html) includes some background info, but let me know if anything is unclear. The code...

Thank you for doing this. This is a really nice enhancement and I am glad you shared the code. I still feel like this is outside the scope of the...

A helper package is a great idea. I thought about suggesting that, but it seemed like an overkill for one function. Makes more sense as you add more functionality.

Thank you for the suggestion. Currently, the package is just reformatting the original MSigDB for easier access. This might be outside the scope, but certainly worth considering. To clarify, this...

Yes, the original non-alphanumeric characters and capitalization are probably the most valuable aspect, and that can't be automatically fixed.

My concern with that approach is that it gives you different results than the BED file. I assume "chr21.refseq.hg19.bed" and "chr21.refseq.hg19.gtf" should be comparable.