Please contact me to add your plugin to the list (or to remove it). Plugins mentioned in published papers will be added as I find them, otherwise plugins will only be added on request and with the creator's permission.
| Plugin | Description |
|---|---|
| Base | Provides basic functionality for more complex plugins to extend |
| Data | Extends the base plugin to provide communications and data handling methods |
| Track | Extends the data track to add renderimg methods. It's best to extend this for custom plugins |
| Masks | For showing simple 1d masks (eg, from RepeatMasker) |
| SNPs | For showing SNPs in the genome |
| MethylCytosine | For showing cytosine methylation sites. Each site shows extent and context (CG, CHG, CHH) |
| WGTA | For data from whole-genome tiling arrays. Supports multiple data series |
| GeneModels | For gene model annotations using GFF style data |
| ShortReads | For showing short DNA reads from deep sequencing |
| Stacks | For deep sequencing data. Shows read depth and call composition by base |