Marcel Schilling

@jamalstat: If you follow the link @yihui provided you find links to two different sites: 1. [RSudio Community](https://community.rstudio.com/c/R-Markdown/10) 2. [Stack Overflow](https://stackoverflow.com/questions/tagged/r+bookdown)

@marwa38: IIRC pandoc can convert DOCX to Markdown. I have used it in the past with default settings and while it did require substantial re-formatting I think it saved me...

What OS/shell/terminal are you using? AFAIC this is not the job ob the TUI application but should be handled by the terminal.

IMHO if `/usr/bin/env python` doesn't point to the 'correct' Python path, that's a problem with your system configuration. Hard-coding it to `/usr/bin` will break it on all system installing Python...

@WhyNotHugo > Do any other packages work around this issue? I only know this issue from packaging for GNU Guix where the 'solution' is to 'fix' the shebangs by hardcoding...

@hamdav: > but I want to get the conda python when I type python in the terminal, right? I don't know what you want. Python was note developed with the...

@BioBox > There was a button on github that said "Update Branch" and it made the "Merge branch 'master' into master" commit. Don't know what was up with that. I...

Have you tried setting `return.only.var.genes=FALSE` for `SCTransform`? If you only keep variable genes in the `SCT` layer, you might have data for different subsets of genes in the different Seurat...

@stefanonard85: I was more referring to the general issue of 'subscript out of bounds when trying to merge [...] SCTransform[ed] Seurat objects'. @mariavam just told me earlier today that they...

Thank you. I can confirm that copying the 'mature' sequences to the 'precursor' FASTA results in miRDeep2 picking up the RNA spike-ins for quantification.