dPeak: High Resolution TFBS Identification using ChIP-exo, PET and SET ChIP-Seq Data


dPeak is a high resolution transcription factor binding site (TFBS) identification
(deconvolution) algorithm. dPeak implements a probabilistic model that accurately
describes ChIP-exo and ChIP-Seq data generation process for both the SET and PET assays.
For SET ChIP-Seq data, dPeak outperforms or performs comparably to the state-of-the-art
high resolution ChIP-Seq peak deconvolution algorithms such as PICS, GPS, and GEM.
When coupled with PET ChIP-Seq data, dPeak significantly outperforms SET-based analysis
with any of the current state-of-the-art methods. For ChIP-exo data, dPeak outperforms
or performs comparably to the state-of-the-art algorithms such as GEM and Apex.


SOFTWARES

Please download dpeak R package from the link below.

'dpeak' package (ver 1.0.0)

You can install the dpeak R package with the command:

> R CMD INSTALL dpeak_1.0.0.tar.gz

The R package vignette below provide overview of the dpeak R package
and describes its command lines with real ChIP-Seq data examples.

Vignette

Developmental version of dpeak R package is available in GitHub:

GitHub dPeak page


REFERENCES

Chung, Dongjun, Dan Park, Kevin Myers, Jeffrey Grass, Patricia Kiley,
Robert Landick, and Sunduz Keles (2013). “dPeak: High resolution identification
of transcription factor binding sites from PET and SET ChIP-Seq data.”
PLoS Computational Biology, 9(10): e1003246.

Chung, Dongjun, Irene Ong, Jeffrey Grass, Robert Landick, Patricia Kiley,
and Sunduz Keles (2013). “High resolution identification
of protein-DNA binding events using ChIP-exo data with dPeak.” (in preparation)