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Revision as of 17:34, 30 January 2006
Plugins are sets of pluggable components for geWorkbench.
Below is the list of available plugins.
Contents
Microarray Visualization
| Plugin | Description | Compatibility |
|---|---|---|
| caBIO Pathways | Displays BioCarta pathway diagrams for selected genes. | TBD |
| Color Mosaic | Displays heat maps for microarray expression data, organized by phenotypic or gene groupings. | Verified to work on 3.0 |
| 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 |
| Expression Value Distribution | provides a distribution plot of the expression values for one or more microarrays. | TBD |
| Marker Annotations | Supports the retrieval of CGAP annotations for genes within a marker panel. | TBD |
| Microarray Panel | This 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 |
| Scatter Plot | --. | 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 |
Normalizers
| Plugin | Description | Compatibility |
|---|---|---|
| Array-based centering | Subtracts 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 |
| Quantile | ?. | TBD |
| Housekeeping | The system is able to normalize data based on the values of user selected house-keeping genes. | TBD |
Annotation
| Plugin | Description | Compatibility |
|---|---|---|
| Dataset History | -- | ? |
| Experiment Information | -- | ? |
| Image Annotation | -- | ? |
| Marker Annotation and Pathway Listing | -- | ? |
Network Generation
| Plugin | Description | Compatibility |
|---|---|---|
| Reverse Engineering | ??. | ? |
| Cytoscape | ??. | ? |
Analysis
| Plugin | Description | Compatibility |
|---|---|---|
| Hierarchical Clustering | Hierarchical clustering groups markers into clusters on the basis of similarities in their expression profiles to form a hierarchical tree that can be viewed in the Dendrogram View window. | ? |
| Self Organizing Map (SOM) | Displays heat maps for microarray expression data, organized by phenotypic or gene groupings. | ? |
| T Test | -- | ? |
Sequence Alignment
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Pattern Discovery
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Filters
| Plugin | Description | Compatibility |
|---|---|---|
| Affy detection call | (Affymetrix data only) Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. | TBD |
| Deviation | Sets all markers whose measurements deviate below a given value across all microarrays as missing. | ? |
| Expression threshold | Sets all markers whose measurements are inside (or outside) a user-defined range as missing. | ? |
| Genepix Flag Filter | --. | ? |
| Missing values | Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. | TBD |
| 2-channel threshold | (Genepix data only) Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. | TBD |
