RNA half-life calculation using SlamDunk

Question

[Caleb]

I want to use SlamDunk to calculate transcriptome wide RNA half-lives after SLAM-seq, but the pipeline itself does not calculate half lives. In the paper describing SlamDunk they said they use the minpack.lm package in R to calculate the half-lives using the integrated rate law for a first order expression. I'm not entirely sure how to use the package, particularly in the context of SlamDunk. Does anyone have a script for using this package with SlamDunk, or at least some sort of example or tutorial about it's use for SlamDunk?

[lech.kaczmarczyk]

Hi Caleb, I'd like to embark on using SLAM-seq. I was wondering if you made any progress with the half-life calculations in R? Cheers, Lech

[EVR]

Hi @lech.kaczmarczyk @Caleb,

Were you people able to compute RNA-half lives from SLAMdunk pipeline. If yes, I would be grateful, if you could share the pipeline how you achieved it. Thanks in advance.