#Nucleotide Density Plugin

This is a JBrowse plugin

Allows the user to create multi-lined heatmaps for differente nucleotide contexts. Usr can set the color for each context. Initial intended use is for CG, CHG, and CHH frequency.

##Special Thanks Special thanks to [Colin] who inspired components of this plugin. Particularly, the GC Content plugin (for the stor class) and Multi BigWig plugin (for multiple density tracks). Additionaly, special thanks for Erik Lyons for the color dialog.

##Install

For JBrowse 1.11.6+ in the JBrowse/plugins folder, type:
git clone https://github.com/bhofmei/jbplugin-nucdens.git NucleotideDensityPlugin

or

downloaded the latest release version at releases.
Unzip the downloaded folder, place in JBrowse/plugins, and rename the folder NucleotideDensityPlugin

##Activate

Add this to jbrowse.conf under [GENERAL]:

    [plugins.NucleotideDensityPlugin]
    location = plugins/NucleotideDensityPlugin

If that doesn't work, add this to jbrowse_conf.json:

    "plugins" : {
        "NucleotideDensityPlugin" : { "location" : "plugins/NucleotideDensityPlugin" }
}