This is a really well built GUI for DE. I have tried others and this one appears to allow greater depth and breath of analytical outputs, and especially ease of file uploads and parsing.
Couple of questions though: In many modules like the low expression gene filtering, DESEq2 or limma, very limited parameters are adjustable on the GUI.
1. For example, which module (.R file) is the one for filtering low expressed genes?
2. Is it possible to choose different normalization methods? TMM, etc....
3. Where are the .R files for DESEQ2 and Limma and what parameters can be adjusted.
I understand that the reason is to be conservative on the unattended app, but I guess working with the source code it would be a little helpful to allow flexibility.
Thanks again for a great application,