Question: paired design in bulk ATAC-seq analysis

[AlexBlais74]

Hello
I am curious if chromVAR would allow the use of paired designs, in the function differentialDeviations.
Our dataset compares two cell types isolated from 6 patients. When we perform differential DNA accessibility testing, we see a big improvement (in number of DARs identified) when we use a paired (by patient) design. I was wondering if chromVAR would offer this level of flexibility.

Thanks
Alex