From: Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential
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]
