Skip to content

Latest commit

 

History

History
63 lines (51 loc) · 1.97 KB

plugins.md

File metadata and controls

63 lines (51 loc) · 1.97 KB
Raw

status of plug-ins

The plug-ins provide various features to geWorkbench. In principle, they are not required for the platform itself. There are two main groups: the first group is tightly tied to the general workflow and data types of geWorkbench, which in turn includes two categories: analysis and visualization; the second group, called 'standalone', is only presented via the geWorkbench user interface.

list of analysis plug-ins

  1. anova: on
  2. aracne: on
  3. cnkb: on (There is a standalone version of this plug-in as well.)
  4. t test: on
  5. gene ontology: on
  6. hierarchical clustering: on
  7. marina: on
  8. markus: not fully functioning

list of visualization plug-ins

  1. anova result: on
  2. aracne result: on
  3. cnkb result: on
  4. cytoscape: on
  5. dendrogram: on
  6. GO result: on
  7. marina result: on
  8. markus result: not fully functioning
  9. molecular structure viewer: on
  10. PDB file viewer: on
  11. t test result: on
  12. tabular microarray viewer: on

list of 'standalone' plug-ins

  1. cnkb: on (Note that there is a regular analysis version as well.)
  2. lincs: not fully functioning
  3. pbqdi: not fully functioning
  4. TCGA Driver-Gene Inference: on

customized visualization/widgets

Depending on the level of customization, we can group the visualization into three categories: [A] fully customized widgets, [B] abstract JavaScript component, and [C] addons.

  1. barcode table - [B]
  2. citrus diagram - [B]
  3. cytoscape - [B]
  4. dendrogram - [A]
  5. molecular viewer - [B]
  6. t test result viewer - [C] (highchart)
  7. cnkb result viwer - [C] (highchart)

barcode table

This is part of MsViper result viewer. MsViper is a synonym of marina.

citrus diagram

Part of GeneBasedQueryAndDataIntegration (TCGA Driver-Gene Inference).

cytoscape

Part of NetworkViewer.

dendrogram

Used in hierarchical clustering result viewer. References from HierarchicalClusteringResultUI, DisplayOptionCommand, and SubsetCommand.

molecular viewer

Part of PDBViewer (molecular structure viewer).