Table 1 Overview and guidance on common and selected R packages used in DNA methylation pipelines as a starting point for making decisions based on the desired estimate. See Heiss et al. [4] for information on the differences between Illumina microarrays and bisulfite sequencing. See table 3 for information on M-values and Beta-values

Full pipeline (DMCs and DMRs)

BioMethyl\(^1\)

M-values, Beta-values (BS-seq\(^{\dagger }\))

minfi\(^{2}\)

M-values, Beta-values

ChAMP\(^{3}\)

M-values, Beta-values

RnBeads\(^{4}\)

M-values (BS-seq\(^{\dagger }\))

metilene\(^{5}\)

Beta-values (BS-seq\(^{\dagger }\))

Preprocessing\(^{\ddagger }\)

ComBat (sva\(^6\))

M-values (BS-seq\(^{\dagger }\))

melon (wateRmelon\(^{7}\))

Beta-values

BMIQ (wateRmelon\(^{7}\))

Beta-values

SWAN (missMethyl\(^{8}\))

Beta-values

CellDMC (EpiDISH\(^9\))

lm (stats)

Beta-values

Detect differentially methylated single CpG sites (DMCs)

champ.DMP (ChAMP\(^3\))

lmFit (limma\(^{10}\))

M-values, Beta-values

dmpFinder (minfi\(^2\))

lmFit (limma\(^{10}\))

M-values, Beta-values

calDEG (BioMethyl\(^1\))

t-test

M-values, Beta-values

varFit (missMethyl\(^{8}\))

lmFit (limma\(^{10}\))

M-values

DMLtest (DSS\(^{11}\))

Count values (BS-seq\(^{\dagger }\))

Detect differentially methylated regions (DMRs)

bumphunter (bumphunter\(^{12}\))

lmFit (limma\(^{10}\))

M-values(BS-seq\(^{\dagger }\), after transformation)

champ.DMR (ChAMP\(^3\))

bumphunter (bumphunter\(^{12}\))

M-values

dmrcate (DMRcate\(^{13}\))

lmFit (limma\(^5\))

M-values (BS-seq\(^{\dagger }\))

gometh (missMethyl\(^{8}\))

M-values, Beta-values

BSmooth (bsseq\(^{14}\))

Beta-values (BS-seq\(^{\dagger }\))