differential analysis resolution: select the resolution of differential analysis. If site resolution is selected, differential analysis will be applied at each site. If transcript resolution is selected, the differential analysis will be applied at each transcript.

differential analysis scale: select the scale of differential analysis. If search region is selected, the differential analysis will be applied in the inputed region and users should ensure the column of genomic region of selected items be the same. Users can filter it through the search tool provided by the table of Search Result Overview. If entire genome is selected, the differential analysis will be applied in the whole genome.

differential analysis method: select the method of differential analysis. There are 5 methods including t-test, minfi, samr, edgeR and entropy. If entropy is selected, the differential analysis will be applied through method of Shannon entropy from QDMR. If t-test is selected, the differential analysis will be applied through Student's t test. And the method of entropy can be used across more than two groups.

Significant p-value: select the significant p-value for the differential analysis. If the result is less than selected p-value, the transcript or methylation site will be grouped to DMR (differentially methylated region). Otherwise, it will be grouped to N-DMR (not differentially methylated region).

absolute methylation difference: this option is used to filter the differentially methylated region together with the p-value.