dpeak

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 mosaics package at http://github.com/dongjunchung/dpeak. To install the development version of dpeak, it’s easiest to use the devtools package:

#install.packages("devtools")
library(devtools)
install_github("dongjunchung/dpeak")

References

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.

Welch R, Chung D, Grass J, Landick R, and Keles S (2017), “Data exploration, quality control, and statistical analysis of ChIP-exo/nexus experiments,” Nucleic Acids Research, 45(15): e145. (* Joint first authors)