DESeq2 is an R package that is used to normalize, visualize, and differentially analyze count data. By using shrinkage estimation for dispersions and fold changes it enables quantitative analysis focused on the strength rather than just the presence of differential expression. Pluto uses the latest DESeq2 package to perform differential expression.
Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014). https://doi.org/10.1186/s13059-014-0550-8