Bayesian Estimation of Temporal Regulation-RNASeq

Question

[Sreeraj Thamban]

Hi everyone recently I came across this paper where they used Bayesian Estimation of Temporal Regulation to analyze their time course RNASeq data. Can anyone suggest a good package in R or other software to do the same?

Answer 1

[andrew.j.skelton73]

When looking at a whole time course, you can look at the timecourse package which implements the Hotelling T2 test. Alternatively, you could use packages such as Limma to look for non-linear trends via splines using functions such as ns (natural cubic spline). I did something similar to this and got some great advice from Aaron Lun on Bioconductor support, so this post may be of some help.