SCnorm requires estimates of expression, but it is not specific to one approach. Estimates may be obtained via RSEM7, HTSeq12, or any method providing un-normalized counts per feature. Let
Yg,
j denote the log nonzero expression count for gene
g in cell
j for
g = 1,...,
m and
j = 1,...,
n;
Xj denote log sequencing depth for cell
j. Motivation for considering nonzero counts is provided in
Supplementary Note 3 and
Supplementary Figures 12 and
13.