For official R package to run models and generate figures, please see: https://github.com/jakeyeung/TissueCiradianAnalysis
These are scripts I used for all downstream analyses in Yeung, Mermet, et al 2018.
A review of some of the insights we gained from the analyses can be found in Yeung, Naef et al 2018.
This is a dump of many scripts, so I will soon link to an R package that highlights some of things you can do to analyze circadian gene expression across tissues.