Features suggestions

[bolak92]

Hello,

First of all, fantastic work with the pipeline implementation.

There are some functionalities, that I'd love to see in the pipeline, which can initiate some collaboration as well.

1. having the VSN normalization as an option to compare in the normalization methods
   here is the VSN documentation.

2. having options to run differential expression, mainly using the DEqMS algorithm:
   here is the DEqMS in R documentation
   getting the outputs as csv or tables can be of great benefit here as well.

3. utilizing the aGOtool for the GO Enrichment analysis: https://agotool.org/API_Help

I hope this feedback helps and let me know if further discussions are needed.

Regards, Bola

[siheming]

Hey, unfortunatly I am not really developing this package actively anymore and dont have much free time on my hands, but I can give you a few pointers what to do where, if you are interested in implementing these features yourself.