Man pages for ShanEllis/methylarking
Analyzing RRBS Data
| annotateGenes | Annotate genomic position using bumphunter's matchGenes |
| bootstrap | Boxplot of single sites from output from DMS Analysis |
| bootstrap_array | Boxplot of single sites from output from DMS Analysis |
| bootstrap_noout | Boxplot of single sites from output from DMS Analysis |
| boxplot_DMR | Boxplot of regions from output from DMR Analysis |
| boxplot_DMS | Boxplot of single sites from output from DMS Analysis |
| boxplot_VMR | Boxplot of regions from output from VMR Analysis |
| Circos | QQ plot of all sites from DMS Analysis |
| CpGPie | Pie Chart: CGI Annotation |
| GenePie | Pie Chart: GeneAnnotation |
| hyper | Get Hypermethylated Sites |
| hypo | Get Hypomethylated Sites |
| karyo | Karyogram: |
| manhattan | Manhattan plot of all sites from DMS Analysis |
| mean.meth | Mean Methylation Difference - by case-control |
| multiplot | Multiplot function |
| obs | QQ plot of all sites from DMS Analysis broken down by Mean... |
| QQplot | QQ plot of all sites from DMS Analysis |
| runbumphunter | Run bumphunter to obtain DMRs (parameters stolen straight... |
| runDVS | DVS Analysis |
| runlimma | DMS Analysis |
| sitesperchr | Plot number of sites by chromosome |
| volcano | Volcano plot of all sites from DMS Analysis |
