ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data.

Giorgos MinasHiroshi MomijiDafyd J JenkinsMaria J CostaDavid A RandBärbel Finkenstädt

Published in: BMC bioinformatics (2017)

The ReTrOS toolbox allows users to analyse gene and/or protein expression time series where, with appropriate formulation of prior information about a minimum of kinetic parameters, in particular rates of degradation, users are able to infer timings of changes in transcriptional activity. Data from any organism and obtained from a range of technologies can be used as input due to the flexible and generic nature of the model and implementation. The output from this software provides a useful analysis of time series data and can be incorporated into further modelling approaches or in hypothesis generation.

Keyphrases

electronic health record
big data
gene expression
transcription factor
copy number
data analysis
primary care
drug delivery
machine learning
heat shock
social media