Wimtrap: Integrative tools to predict the location of trancription factor binding sites, with advanced supports for Arabidopsis thaliana and Solanum lycopersicum
Purposes of the package
Wimtrap is an R package for the prediction of Transcription Factors Binding Sites (TFBS) and corresponding genes targets. It is particularly convenient to preselect candidates targets of TFs of the plant-model Arabidopsis thaliana and Solanum lycopersicum in specific contexts (organs, growth stages, treatments), through the implementation of a ready-to-use model that improves the accuracy of the predictions of TFs in comparison with the popular method that consists to only apply a pattern-matching analysis. The approach, that takes into account epigentic data, can be generalized to any organism.
Install and use Wimtrap
Wimtrap is a R-package deposited on github. It can be installed by entering the following in R:
dependencies = TRUE,
build_vignettes = TRUE)
To use Wimtrap, please follow the vignette.
Quentin Rivière, Madalina Ciortan, Massimiliano Corso, Nathalie Verbruggen and Matthieu Defrance (2021).