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Table 3 Packages and methods for methylation differential analysis

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 [100102]
- Kolmogorov-Smirnov test [104]
CpGAssoc permutation test [101]
RnBeads, IMA and minfi empirical Bayes [102, 103, 105]
bumphunter and minfi bump hunting [105, 106]