Table 2.
Example visualization approaches for epigenome-wide DNA methylation data.
| Method | Utilities | Implementation | Application/comments |
|---|---|---|---|
| MethVisual | Exploratory data analysis and visualization | R | For bisulfite sequencing data, not genome-wide DNA methylation data (i.e., from Illumina 450K array) |
| methyAnalysis | Data analysis and visualization | R | For bisulfite sequencing data, not genome-wide DNA methylation data |
| Methylation plotter | Visualization only | Web | User-friendly, more general descriptive analysis and visualization; more appropriate for small number of samples compared to large sample size of individuals |
| MethTools | Exploratory data analysis and visualization | R and web | For bisulfite sequencing data, not genome-wide DNA methylation data |
| MethylMix | Data analysis and some visualization | R | For genome-wide DNA methylation data; implements specific beta mixture model and may not have full flexibility desired |
| IMA | Data analysis and some visualization | R | For common exploratory analysis of genome-wide DNA methylation data; standard pipeline may limit flexibility |
| CoMET | Visualization only | R and web | Appropriate for various types DNA methylation data |
| Minfi | Data analysis and some visualization | R | For genome-wide DNA methylation data; offers fair amount of flexibility |
| Independent coding | Data analysis and visualization | R | Appropriate for various types of DNA methylation data; specific to analysis and data needs; independent of data input and format requirements of packages but may require more analysis time and skill compared to other methods |