single cell or bulk data?

[mingyudu]

Hi,

I am trying to use Clipper to do the differential analysis on my data, which is a single-cell dataset collected from multiple subjects. I found the example data included in the package only has 3 columns(replicates). I wonder if this is a bulk-seq data. If this is the case, could you please clarify whether the code in the vignettes remains applicable to analyzing single-cell data collected from multiple subjects?

Thanks!

[xcggates]

Hello Mingyu,

Thank you for using Clipper! The example data was bulk single cell RNA seq data. However, Clipper can be used on single cell RNA-seq data. The tutorial on our website can be applied directly to single cell data: http://shiny2.stat.ucla.edu/Clipper/ In your case, do you need to do clustering first to divide the cells into groups and do differential analysis between groups? if so, you can refer to our latest method clusterDE, which use Clipper in the differential analysis: https://github.com/SONGDONGYUAN1994/ClusterDE