Difference between revisions of "Plugins"
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|Color Mosaic||Displays heat maps for microarray expression data, organized by phenotypic or gene groupings.||Verified to work on 3.0
 
|Color Mosaic||Displays heat maps for microarray expression data, organized by phenotypic or gene groupings.||Verified to work on 3.0
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==Network Generation==
 
==Network Generation==
  
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|Color Mosaic||Displays heat maps for microarray expression data, organized by phenotypic or gene groupings.||Verified to work on 3.0
 
|Color Mosaic||Displays heat maps for microarray expression data, organized by phenotypic or gene groupings.||Verified to work on 3.0
 
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==Analysis==
 
==Analysis==
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|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.||Verified to work on 3.0
 
|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.||Verified to work on 3.0
 
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|Self Organizing Map (SOM)||Displays heat maps for microarray expression data, organized by phenotypic or gene groupings.||Verified to work on 3.0
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== Sequence Alignment==
 
== Sequence Alignment==
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== Pattern Discovery==
 
== Pattern Discovery==
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== Filters==
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{|style="border: 1px solid lightGray"
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!Plugin||Description||Compatibility
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|Expression threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
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|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
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|Missing values||Discards all markers that have “missing” measurements in at least n microarrays, where n is defined by the user. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
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Revision as of 15:47, 30 January 2006

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 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

Annotation

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
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. Verified to work on 3.0
Self Organizing Map (SOM) Displays heat maps for microarray expression data, organized by phenotypic or gene groupings. Verified to work on 3.0

Sequence Alignment

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Pattern Discovery

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Filters

Plugin Description Compatibility
Expression threshold Sets all markers whose measurements are inside (or outside) a user-defined range as missing. ?
Deviation Sets all markers whose measurements deviate below a given value across all microarrays as missing. ?
Missing values Discards all markers that have “missing” measurements in at least n microarrays, where n is defined by the user. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. TBD
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