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 | ||
| − | |||
| − | |||
* 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]] === | ||
| Line 28: | Line 31: | ||
* 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
Contents
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)
