André F. Rendeiro

I understand the purpose and wouldn't particularly mind it as long as there wouldn't be surprises like above. If no immediate added value, maybe it is better to switch back...

No issue with combining them into `bam_to_fastq`. There seems to be one difference in keeping unpaired reads and then on the interface, where one requires a prefix that is then...

I'd say let's keep/adopt the Python convention: `snake_case`/`lower_case_with_underscores` everywhere.

So the thing is, I'm not using that (and other functions) anymore. I don't think it makes sense to either blindly change or remove functions I'm not using if I...

You're absolutely right. I can also try to handle this when I have a go at sorting out the naming scheme of the remaining NGSTk functions. Regarding SPP, I have...

Just realized the reason for the different order in parameter between MACS2 and SPP peak calling functions is that MACS2 is able to call peaks without control and therefore the...

Those numbers are taken straight from here: https://github.com/taoliu/MACS I guess one could be more accurate, but I wouldn't think it is so critical.

Actually I currently don't know why the command was written in such a complicated way initially (perhaps derived from another use case) but I think this should do it: ```python...

I have no preference for either, you can always use some sort of regex to get whatever files, no? The `find` command is super powerful, I use it all the...

Yeah, I know it is not simple and could even potentially put a lot of stress on your end. But tools like Enrichr really implemented it well (http://amp.pharm.mssm.edu/Enrichr/help#api) and have...