Plugins are sets of pluggable components for geWorkbench.
Below is the list of available plugins.
Microarray Visualization
| Plugin |
Description |
Compatibility
|
| Color Mosaic |
Displays heat maps for microarray expression data, organized by phenotypic or gene groupings. |
Verified to work on 3.0
|
| caBIO Pathways |
Displays BioCarta pathway diagrams for selected genes. |
TBD
|
| Dendrogram |
A tree-structured diagrams reflecting the results of hierarchical clustering analysis. |
TBD
|
| Expression Profiles |
Displays the expression of genes across several arrays/ hybridizations. |
TBD
|
| Image Viewer |
Mechanism to display snapshot images taken in the application. |
TBD
|
| Marker Annotations |
Allows users to retrieve and display CGAP annotations for genes within a marker panel. |
TBD
|
| Microarray Panel |
The image displays color-coded levels of gene expression,using a color scale varying gradually from red (up-regulated) through black (no change) to green (down-regulated). |
TBD
|
| SOM Clusters |
Displays the results of self-organizing map cluster analysis. |
TBD
|
| Tabular Microarray Panel |
Presents the numerical values of the expression measurements in a table format; each row represents an individual probe and the columns display the signal and background intensities and intensity ratios. |
TBD
|
Normalizer
| Plugin |
Description |
Compatibility
|
| Array-based centering |
Displays heat maps for microarray expression data, organized by phenotypic or gene groupingsSubtracts the mean (median) measurement of a microarray from every measurement in that microarray. |
TBD
|
| Marker-based centering |
Subtracts the mean (median) measurement of a marker profile from every measurement in the profile. |
TBD
|
| Mean-variance normalizer |
For every marker profile, the mean measurement of the entire profile is subtracted from each measurement in the profile and the resulting value is divided by the standard deviation.
|
TBD
|
| Missing value calculation |
Replaces every missing value with either the mean value of that marker across all microarrays or with the mean measurement of all markers in the microarray where the missing value is observed.
|
TBD
|
| Threshold Normalizer |
All data points whose value is less than (or greater than) a user-specified minimum (maximum) value are raised (reduced) to that minimum (maximum) value. |
TBD
|
Annoatation
| Plugin |
Description |
Compatibility
|
| Color Mosaic |
Displays heat maps for microarray expression data, organized by phenotypic or gene groupings. |
Verified to work on 3.0
|
Network Generation
| Plugin |
Description |
Compatibility
|
| Color Mosaic |
Displays heat maps for microarray expression data, organized by phenotypic or gene groupings. |
Verified to work on 3.0
|
Analysis
| Plugin |
Description |
Compatibility
|
| Color Mosaic |
Displays heat maps for microarray expression data, organized by phenotypic or gene groupings. |
Verified to work on 3.0
|
