Table 2 JBrowse plugins
From: JBrowse: a dynamic web platform for genome visualization and analysis
Plugin name | Plugin description |
|---|---|
RegexSequenceSearch | Allows the user to enter a simple sequence motif of regular expression, then creates a new feature track showing matches to this motif. Illustrates implementation of JBrowse menu extensions and popups (with CSS), creation of a new track, access of the reference sequence, and dynamic creation of features based on client-side computation |
NeatHTMLFeatures | Extends HTMLFeatures tracks to render introns using the standard cartoon representation of a “hat”-shaped elbow line and features with gradient “tube” effect. Illustrates the implementation of custom glyphs. Draws the intron using Scalable Vector Graphics (SVG) |
NeatCanvasFeatures | The analog of NeatHTMLFeatures for CanvasFeatures tracks |
HideTrackLabels | Extends the toolbar to implement a new button that hides track labels. Illustrates the implementation of toolbar buttons |
DebugEvents | Logs all milestone and globally published events to the browser’s JavaScript console. Illustrates the use of plugins for debugging and subscription to dojo/topic events |
CategoryUrl | Adds a new ‘category’ URL parameter that displays all tracks in a particular category. Illustrates the implementation of new URL parameters |
PubAnnotation | Allows JBrowse to display text annotations from PubAnnotation. Illustrates the creation of a new feature store that queries an external repository |