Software
ReTrOS
A MATLAB toolbox for reconstructing and analysing transcriptional activity from gene and protein expression data
by G. Minas, D. Jenkins, H. Momiji, M. Costa, D. Rand, B. Finkenstadt
ReTrOS-switch: Bayesian inference of transcriptional switches and analysis of activation and repression timings.
ReTrOS-smooth:
kernel smoothing reconstruction with bootstrapping to account for measurement error and parameter uncertainty.
TRS
MATLAB toolbox for inferring transcriptional regulation logic from multiple dynamic experiments
by G. Minas, D. Jenkins, D. Rand, B. Finkenstadt
Bayesian inference of the mechanism of transcriptional regulation of a target gene from a number of candidate regulators. The input dataset are required to be dynamic (time-series) and preferably but not necessarily from multiple experimental conditions.
