Table 3.

Packages and methods for methylation differential analysis

Package	Method	References
methyAnalysis	Wilcoxon rank sum test	[100]
methyAnalysis, CpGAssoc, RnBeads, and IMA	t-test	[100–102]
-	Kolmogorov-Smirnov test	[104]
CpGAssoc	permutation test	[101]
RnBeads, IMA and minfi	empirical Bayes	[102, 103, 105]
bumphunter and minfi	bump hunting	[105, 106]