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 | Â | Score | P-value | [11] |
MTC | Sliding window | Direct | Â | 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 | Â | Tag counts with sign change | P-value | [12] |
NEXT-peak | NEXT-peak kernel density | Direct | Poisson per base pair | Likelihood | Estimated binding intensity (2ν) |  |