Table 1.
Comparison between msgbsR and existing DNA methylation pipeline software tools.
| Package | Type of DNA methylation data | Format of files for importing | Filtering outliers and poor quality probes/sequences | Differential methylation analysis |
|---|---|---|---|---|
| msgbsR | MRE-seq | BAM | Yes | Yes |
| ChAMP 39 | Array | IDAT | Yes | Yes |
| minfi 40 | Array | IDAT | Yes | Yes |
| charm 41 | Array | XYS | Yes | Yes |
| methylpipe 42 | WGBS | BAM | Yes | Yes |
| BSmooth 10 | WGBS | BAM | Yes | Yes |
| BiSeq 9 | RRBS/WGBS | bismarkbed2graph output43 | Yes | Yes |
RRBS: reduced representation bisulfite sequencing, MRE-seq: methylation sensitive restriction enzyme sequencing, WGBS: whole genome bisulfite sequencing.