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Table 1 Comparison of DMR calling software

From: Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus

Program

DMR Identification

Execution

Defiant

Weighted Welch Expansion

Binary

BSmooth [23]

Local-likelihood smoothing with binomial test

R

MethylKit [25]

Fisher’s exact test [37] or logistic regression with tiling

R

MethylSig [26]

beta-binomial [64]

R

Metilene [27]

p-value by beta binomial

Binary

MOABS [65]

beta-binomial

Binary

RADMeth [28]

beta-binomial regression

Binary