Table 1.

Summary of methods for identifying regions of altered methylation.

Method	Package name	Platform	Analysis order	References
Bump hunter	Minfi	R	Site-first	Aryee et al. 2014; Jaffe et al. 2012
Comb-P	Comb-P	Python	Site-first	Pedersen et al. 2012
FastDMA	FAstDMA	C++/Python	Site-first	Wu et al. 2013
A-clustering	Aclust	R	Cluster-first	Sofer et al. 2013
Probe Lasso	ChAMP	R	Site-first	Butcher and Beck 2015
DMRcate	DMRcate	R	Site-first	Peters et al. 2015