How to filter ribosomal RNA from scRNA-seq data
In the paper mentioned, we used the ScaleData function in Seurat to regress out the number of reads, Rn45s abundance, and percent ribosomal gene transcripts. Ribosomal genes were found with the regular expression ^Rp[sl][[:digit:]].

tiss &lt;- ScaleData(object = tiss, vars.to.regress = c("nReads", "percent.ribo","Rn45s"))


Here's a fuller notebook, and we'll have a better organized repository soon.