Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data

Table 2

An overview of the characteristics of different Chip-Seq peak detection algorithm.

Algorithm	Profile	Background model	Control sample	Use control to compute FDR
F-Seq	Kernel density estimation (KDE)		√
FindPeaks	Aggregation of overlapped tags	Monte Carlo
SISSRs	Window scan	Poisson	√
QuEST	Kernel density estimation (KDE)		√	√
MACS	Tags shifted then window scan	dynamic Poisson	√	√
CisGenome	Strand-specific window scan	Negative binomial	√	√