XGAP plugins

New tools can be added as 'plugins' to the XGAP UI as described in ​http://www.molgenis.org/wiki/MolgenisPlugin. This typically involves a statement of the form

<plugin name="MyPlugin" type="java.package.MyPluginCode.java"/>

XGAP already has a growing catalog of such plugins. Below these plugins and their status (use, development, planned) are reported. One can find the code plugins in the folder handwritten/java/plugins of XGAP:

DataWizard - to import/export XGAP data files(in use)

MatrixViewer - to view DataElement objects in the form of a matrix (in use)

RqtlCluster - to run R/QTL calculations on a university computer cluster (in use)

Installation of this plugin requires access to a PBS computing cluster.

DataArchiver - to import/export xgap investigations as zip files (in use)

OntologyBrowser - to browse for ontology terms (in use)

Note: performance is still slow as it is based an remote version of the ​EBI Ontology Lookup Service

InvestigationOverview - report of all annotations and data in one investigation (in use)

MatrixRemove - to remove a whole matrix (in use)

MatrixRplot - minimal visualisations of data matrices (in use)

KEGGConverter - to convert identifiers using KEGG orthologs (in use)