This repository provides the toolkit for a statistical inference mathod in order to estimate reaction constants of simple Birth-Death process with time delay for the paper on Choi B, Cheng YY, Cinar S, Ott W, Bennett MR, Josic K†, Kim JK†, Bayesian inference of distributed time delay in transcriptional and translational regulation, Bioinformatics (2019). The Gamma distribution is used for a delay time distribution, but it can be easily modified to other distribution. The code infers shape and rate parameter of gamma delay distribution along with reaction constants from timeseries data.
File description:
Birth.Death.Delay.R: R code for a statistical inference for Birth-Death process with delay
YFP1.rda: R example data for experiment data set 1 (40 trajectories)
YFP2.rda: R example data for experiment data set 2 (29 trajectories)
YFP1.rda: R example data truncated at T=22 of YFP1
YFP1.rda: R example data truncated at T=22 of YFP2