Kristoffer Vitting-Seerup
Kristoffer Vitting-Seerup
Closing due to no activity. If you respond I will open it again :)
Thanks for reaching out! I will put it on the to do list but unless it get a lot of upvotes it is low priority as IsoformSwitchAnalyzeR have been round...
Thanks for eaching out :-) Just for clarity StringTie (and StringTie2 - they are now merged so only one exists) can create the quantification files by setting the `-eB` flag....
I agree. Could you email me the GTF so I can update `importGTF` ? I would naturally keep it confidential and only use it for debugging.
Could you try and use IsoformSwitchAnalyzeR v 1.16.03 or newer?
Closing due to no activity. If you respond I will open it again :)
Unfortunately it is a bug - you need to update to 1.11.3 via this command: ``` if (!requireNamespace("devtools", quietly = TRUE)){ install.packages("devtools") } devtools::install_github("kvittingseerup/IsoformSwitchAnalyzeR", build_vignettes = TRUE) ```
That sounds very strange. Did you try restarting R after installing IsoformSwitchAnalyzeR 1.11.3? That is sometimes necessary for R to use the updated verstion of the R package.
I think you migth be suplying the entire list list to the `isoformCountMatrix` instead of the count matrix?
Closing due to no activity. If you respond I will open it again :)