Saket Choudhary

For now, I would recommend the fix you have in place. It is slightly tricky to deal this internally given the passed in argument could be anything (SRP/SRR/SRX/GSM etc.). The...

This is good idea! Paging @bscrow if he is willing to help, else I will add it to my list of ToDos.

Thanks for the suggestion! We will have some updates soon.

The current implementation of `vst.flavor` does not support `batch_var` and will be added in a future release.

Hi @TeodoraTockovska, while in principle you can reverse the regression model, there are caveats. Can you elaborate on your use case?

I see. The pearson residuals that are returned are not scaled, so you should be able to use them as it is, unless I ams misunderstanding the interpretation of scaling...

Many thanks! Since the latest build is at [104](http://ftp.ensembl.org/pub/release-104/gtf/canis_lupus_familiaris/), we can probably use an updated gtf

Thanks @Alex-Nesta and @xf78 for reporting the issue. I will try to have a fix soonish. In the meantime, can you check if the data you need is here: https://github.com/saketkc/gencode_regions/tree/master/data...

Hi @sixone11, the introns.bed will contain all the introns. We are revamping this repositry to make it easier to get the first intron, last intron etc. I hope that helps!

Thanks for the report. We are aware of this and will work on improving the speed. It can particularly be slow if there are multiple large datasets since the model...