Dependency and preprocessing requirements?

[nynkekatinka]

Hi everyone,

I like the concept of your tool, especially the statistical soundness, but I have some questions regarding preprocessing of the data. I couldn't find in your paper about normalization and logtransforming the GEM as per usual in scRNA-seq experiments. I read in one of the supplementary materials that you normalized the GEM before and logtransformed the degree matrix. I was wondering if you tested how alterations in preprocessing the data influences the node degrees in the eventual node degree matrix? Similarly, I was wondering how you chose the boxsize 1.5 as a default, given that this number is quite different from SINUM which is my main point of reference.

Thank you in advance!