R function (Package) | Estimates come from | Used input |
---|---|---|
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\(^{\dagger }\)) |