Partek Genomics Suite enables you to visualize each probe and compare the methylation between the groups at a single CpG site level.
Figure 1. Browsing to location from spreadsheet with differentially expressed genes
Figure 2. Viewing location in Genome Viewer
The visualization can be supplemented with a special annotation file which can be built using a UCSC annotation file as the basis. Building and viewing the UCSC annotation file is available as an optional section of the tutorial, Optional: Adding UCSC CpG Island Annotations.
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