Fig. 4.

Summary of peak calling and peak differential analysis tools. a Peak callers can be divided into count-based, shape-based, and Markov model approaches. They can be further divided by the statistical methods or models used. b Peak differential analysis tools can be divided into peak set-based and sliding window approaches. Peak set-based methods are divided based on the usage of external peak caller and RNA-seq DE packages. Sliding window methods are divided based on statistical methods or models used. ZINB: zero-inflated negative binomial; HMM: hidden Markov model; DE: differential expression; NB: negative binomial