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Table 1 Summary of programs used for comparison

From: NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data

  Profile Strand specific Statistical model Peak criteria Rank by Ref
HPeak Sliding window Indirect Hidden Markov model Tag counts Tag counts [10]
WTD Sliding window Direct   Score P-value [11]
MTC Sliding window Direct   Score P-value [11]
CisGenome Sliding window Indirect Binomial Tag counts Tag counts [9]
MACS Sliding window Indirect Local Poisson P-value P-value [8]
QuEST Gaussian kernel density Indirect Poisson Height threshold Q-value [13]
SISSRs Sliding window Direct   Tag counts with sign change P-value [12]
NEXT-peak NEXT-peak kernel density Direct Poisson per base pair Likelihood Estimated binding intensity (2ν)