heathergeiger

Error about missing scran when run with single-cell reference

12

I am currently trying to run SingleR vs. the counts and labels available here: http://geschwindlab.dgsom.ucla.edu/pages/codexviewer Here is my code to get a log-normalized expression matrix and labels in the appropriate...

Runtime >96h for 500M reads vs. ~2h for 150M read downsample

24

Currently trying to run a very large ADT library (~500M reads) for a CITE-Seq project. First, I tried running on all 500M reads at once, with 8 cores. I got...

Cell barcodes almost completely non-overlapping in vignette

1

I tried running through the vignette for the PBMC 1K dataset. I was able to reproduce a list of 124,716 cell barcodes coming from the kallisto/bus pipeline. However when I...