rHVDM

rHVDM is an R package that predicts the activity and targets of a transcription factor using gene expression time course data. It uses a dynamic and mechanistic model of gene expression to derive the activity profile of a transcription factor based on a small number of known targets, and then predicts other putative targets. The package takes measurement error into account and allows an objective assessment of the robustness of fit.

Topic

Transcription factors and regulatory sites;Microarray experiment

Detail

  • Operation: Gene expression analysis

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.16.0

  • Credit: Biotechnology and Biological Sciences Research Council

  • Input: -

  • Output: -

  • Contact: m.barenco@ucl.ac.uk

  • Collection: -

  • Maturity: Mature

Publications

  • rHVDM: an R package to predict the activity and targets of a transcription factor.
  • Barenco M, et al. rHVDM: an R package to predict the activity and targets of a transcription factor. rHVDM: an R package to predict the activity and targets of a transcription factor. 2009; 25:419-20. doi: 10.1093/bioinformatics/btn639
  • https://doi.org/10.1093/bioinformatics/btn639
  • PMID: 19074958
  • PMC: -

Download and documentation

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