Ángeles Arzalluz-Luque

Hi -no, the matrix in `seurat[["RNA]]@data` is not normalized, so that shouldn't be a problem. Authors only included the raw counts in the data slot. Ángeles

Hi, I just came across a similar problem using the package. I wanted to remove the 50% and 100% labels from the plot for similar reasons, and a little trick...

I've had a similar issue with 0 counts in transcripts, has this been solved yet? I know it's a relatively easy fix to just remove zero counts from the count...

Hi, I've been having similar memory and time issues running a simulation with reportcoverage = TRUE. Has this been resolved yet? Ángeles

In the case of the custom annotation file, the features are not in that order, in fact, my .gtf file only contains the annotation info for the exons. As for...

It is the python3 version. I could always try to download the M10 file again and try, see if the file got corrupted somehow. Concerning the custom annotation, I see...

As you pointed out, I usually use RSEM to estimate expression at the transcript level. However, after reading the paper I was curious to try out BRIE and see whether...

Hi Yuanhua, Has the manual been updated yet with more information about how the count values mentioned in [the first section of the manual](https://brie-rna.sourceforge.io/manual.html#brie-isoform-estimate) are calculated? I'm interested in understanding...