dPeak is a statistical framework for the high resolution identification of protein-DNA interaction sites using PET and SET ChIP-Seq and ChIP-exo data. It provides computationally efficient and user friendly interface to process ChIP-seq and ChIP-exo data, implement exploratory analysis, fit dPeak model, and export list of predicted binding sites for downstream analysis. You can track development of dpeaks package at http://github.com/dongjunchung/dpeak. To install the development version of dpeak, it's easiest to use the devtools package:
Note that GNU Make is a system requirement. For more information on installing GNU Make can be found here: https://www.gnu.org/software/make/. Note as well that fimo and meme are required for use of DpeakMotif. Since these are unavailable on Windows, Windows users will not be able to utilize the DpeakMotif functionality.
Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, and Keles S (2013), "dPeak: High resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data," _PLoS Computational Biology_, 9(10): e1003246.
Chung D, Ong I, Grass J, Landick R, Kiley P, and Keles S (2013). "High resolution identification of protein-DNA binding events using ChIP-exo data with dPeak." (in preparation)