Table 1.

Peak-calling algorithms for ChIP-seq

Name of algorithm	Notable features
MACS [23]	Uses both a control library and local statistics to minimize bias
SICER [14]	Designed for detecting diffusely enriched regions; for example, histone modification
PeakSeq [24]	Corrects for reference genome mappability and local statistics
SISSRs [25]	High resolution, precise identification of binding-site location
F-seq [26]	Uses kernel density estimation