Difference between revisions of "Components"

 
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==== Major Components ====
 
==== Major Components ====
  
 +
* Microaray Panel
 
* Analysis (Hierarchical Clustering, SOM, T-Test, Multi T-Test)
 
* Analysis (Hierarchical Clustering, SOM, T-Test, Multi T-Test)
 
* Filtering (Deviation, Affy detection call, Expression threshold, Genepix Flags, Missing values, 2 channel)
 
* Filtering (Deviation, Affy detection call, Expression threshold, Genepix Flags, Missing values, 2 channel)
 
* Normalization (Housekeeping, Log2 transform, Marker based centering, Mean variance, Array based centering, Missing value, Threshold, Quantile)
 
* Normalization (Housekeeping, Log2 transform, Marker based centering, Mean variance, Array based centering, Missing value, Threshold, Quantile)
 
* Expression Value Distribution
 
* Expression Value Distribution
* Go Terms
 
* Reverse Engineering (should perhaps be broken into seperate components)
 
 
* Scatter Plot
 
* Scatter Plot
 
+
* Tabular microarray
 +
* Volcano plot
  
 
==== Minor Components ====
 
==== Minor Components ====
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=== Additional Components (that pass the [[Plugin certification checklist]]) ===
 
=== Additional Components (that pass the [[Plugin certification checklist]]) ===
  
 +
* Reverse Engineering (should perhaps be broken into seperate components)
 +
* Sequence retriever
 +
* Cytoscape
  
 
=== Components that do not yet pass the [[Plugin certification checklist]] ===
 
=== Components that do not yet pass the [[Plugin certification checklist]] ===
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* caScript (Not yet complete)
 
* caScript (Not yet complete)
 
* Synteny parameters (Does not generate proper dataset subnodes)
 
* Synteny parameters (Does not generate proper dataset subnodes)
 +
* Synteny main panel (Does not receive proper dataset subnodes, function not clear)
 
* Marker Annotations ("Retrieve Annotations" button should be disabled until user makes marker selection)
 
* Marker Annotations ("Retrieve Annotations" button should be disabled until user makes marker selection)
 
* Color Mosaic ("Pat" and "Abs" buttons appear to do nothing)
 
* Color Mosaic ("Pat" and "Abs" buttons appear to do nothing)
 
* Expression Profiles (Performs large computations on event reception and tab selection)
 
* Expression Profiles (Performs large computations on event reception and tab selection)
 
* caBIO Pathways (Function not tied properly to datasets, operation not clear)
 
* caBIO Pathways (Function not tied properly to datasets, operation not clear)
 +
* Go Terms (Interface not clear, needs to be standardized)
 +
* GSEA (Contains 200+ megabytes of additional data)

Latest revision as of 16:31, 2 January 2006

geWorkBench Component List and Status

Core Components (bundled with main application)

Major Components

  • Microaray Panel
  • Analysis (Hierarchical Clustering, SOM, T-Test, Multi T-Test)
  • Filtering (Deviation, Affy detection call, Expression threshold, Genepix Flags, Missing values, 2 channel)
  • Normalization (Housekeeping, Log2 transform, Marker based centering, Mean variance, Array based centering, Missing value, Threshold, Quantile)
  • Expression Value Distribution
  • Scatter Plot
  • Tabular microarray
  • Volcano plot

Minor Components

  • Dataset Annotation
  • Dataset history
  • Experiment info

Additional Components (that pass the Plugin certification checklist)

  • Reverse Engineering (should perhaps be broken into seperate components)
  • Sequence retriever
  • Cytoscape

Components that do not yet pass the Plugin certification checklist

  • Associations (Interface needs to be standardized)
  • caScript (Not yet complete)
  • Synteny parameters (Does not generate proper dataset subnodes)
  • Synteny main panel (Does not receive proper dataset subnodes, function not clear)
  • Marker Annotations ("Retrieve Annotations" button should be disabled until user makes marker selection)
  • Color Mosaic ("Pat" and "Abs" buttons appear to do nothing)
  • Expression Profiles (Performs large computations on event reception and tab selection)
  • caBIO Pathways (Function not tied properly to datasets, operation not clear)
  • Go Terms (Interface not clear, needs to be standardized)
  • GSEA (Contains 200+ megabytes of additional data)