Danny Conrad

addGeneExpressionMatrix incorrectly calculates "Gex_MitoRatio"

1

This is a quick fix but users should know that when doing any kind of multiome analysis, `addGeneExpressionMatrix()` is not accurately calculating `Gex_MitoRatio`. There are two sources of error here...

Is scaleDims scaling along the wrong axis?

4

I read the issue threads #323 & #447 because I've been working a lot with the LSI components of my datasets lately. I think I found the source of the...

cellsnp-lite output not working with Vireo - reporting really high read depths

1

I have a scATACseq dataset where I'm trying to use the mitochondrial reads to demultiplex two mouse strains. When I run cellSNP and cellsnp-lite in mode 2 using what I...

GeneAnnotation & Cis-BP references need to be updated

1

This is somewhere between a bug and a feature request, but posting in Issues so that hopefully users (and future devs) see it: due to its age, ArchR has fallen...