I am using version 1.16.1 of DESeq2. According to the documentation, a Cook's distance cutoff of 0.99 is applied to the results function by default. I looked at the source code in github and this certainly seems to be the case. However, if I get a larger number of significant genes when running the "results" function with default arguments compared to when I explicitly use the argument "cooksCutoff = 0.99". Is version 1.16.1 in Bioconductor up to date with the source code on github? (https://github.com/mikelove/DESeq2). I have not done much digging otherwise.