Lukas Weber

Also leaving a link to the VisiumIO package here (which is in Bioc-devel now) so we have all the links in one place: https://github.com/waldronlab/VisiumIO

Just following up on this - I have been recommended this tool `sam-xlate`, which can convert a BAM from genomic to transcriptomic coordinates: https://github.com/mozack/ubu/wiki However it isn't clear to me...

Oh cool, thanks for this idea, I'll look into this. I am already manipulating the `vcf` file to keep only variants in 3' UTR regions (this greatly speeds up runtime,...

Thanks for this idea. Unfortunately, I don't think it worked in the end. I used Ensembl Variant Effect Predictor (VEP) tool to get the transcriptome ID and position for each...

Happy to join the meeting too. I have filled out the when2meet.

Here are my `.Rproj` settings: ``` Version: 1.0 RestoreWorkspace: Default SaveWorkspace: Default AlwaysSaveHistory: Default EnableCodeIndexing: Yes UseSpacesForTab: Yes NumSpacesForTab: 2 Encoding: UTF-8 RnwWeave: Sweave LaTeX: pdfLaTeX BuildType: Package PackageUseDevtools: Yes...

Ah yes, in this project we have been using 4 spaces for tabs. I usually use 2, so here I have always been hitting tab twice. So yes, if you...

Hi @senbaikang , thanks for this pull request, and apologies that we didn't reply earlier. I'm working through this now for the upcoming Bioconductor release cycle. Could you please let...

Great, thanks for the explanation. So the additional `...` is required for passing additional arguments to the `addImg()` function, that makes sense. Yes, if it is possible to do this...

Great, thank you, yes this additional update looks good for removing the new dependencies. We will continue to work through the rest of the update and will follow up here...