| annotateDMRs | Annotate DMRs |
| CfromFASTAv4 | Extract cytosines from FASTA |
| filterDMRmatrix | filter DMR matrix |
| makeDMRmatrix | Builds a DMR matrix for all samples |
| makeReg | Generates cytosine clusters in genome |
| runjDMRgrid | Run jDMR on binned genome |
| runjDMRregions | Run jDMR for Regions |
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