A signal-noise model for significance analysis of ChIP-seq with negative control.
Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK.
CCAT (Control-based ChIP-seq Analysis Tool) implements a signal-noise model to identify significant ChIP-seq peaks or regions, by comparing a ChIP library and a control library.
Program availability : CCAT3.0.tar.gz
The original paper can be found in here.