finding individual genes with differential stability?

[jackhump]

I'd first like to thank you for providing a useful software package that is both easy to install and has a well-written README. So far, running REMBRANDTS and the CRIES pipeline has been very straightforward and not the useful painful experience I've come to expect from a lot of bioinformatics software.

I'm interested in using REMBRANDTS to look for RNA-binding protein targets that show changes in mRNA stability when those RBPs are depleted. Would you be able to advise on the best practice for extracting the most likely candidates from the stability matrix? I have total RNA-seq samples from mouse spinal cord - wildtype, heterozygous and homozygous for a knockout allele with 3-4 biological replicates for each genotype.

Thank you for your time.