Difference between revisions of "Plugins"
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!Plugin||Description||Compatibility | !Plugin||Description||Compatibility | ||
| + | |Gene Panel ||A subselection of markers which define data views by restricting number of markers shown.||TBD | ||
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| + | |Phenotype Panel ||A subselection of microarrays which define data views by restricting number of arrays shown.||TBD | ||
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!Plugin||Description||Compatibility | !Plugin||Description||Compatibility | ||
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| − | |Dataset History|| | + | |Dataset History||Lists data transformations induced by data-modifying operations.||? |
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| − | |Dataset Annotation||A free text format | + | |Dataset Annotation||A free text format box used by users to annotate data files, projects and images.||? |
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| − | |Experiment Information|| | + | |Experiment Information||Displays any available experiment information associated with a Microarray dataset.||? |
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| − | |Self Organizing Map (SOM)|| | + | |Self Organizing Map (SOM)|| An algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||? |
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Revision as of 15:27, 31 January 2006
Plugins are sets of pluggable components for geWorkbench.
Below is the list of available plugins.
Contents
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 |
| Dendrogram | A tree-structured diagrams reflecting the results of hierarchical clustering analysis. | TBD |
| Dot Matrix | Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions[[.<A - I'm not sure if I should move this to Sequence Analysis]]> | tbd |
| Expression Profiles | Expression of genes across several arrays/ hybridizations. | TBD |
| Expression Value Distribution | 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 | 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 | Expression data is plotted with one marker or microarray on the x-axis and the other on the y-axis (on up to six plots). | TBD |
| SOM Clusters | <A should I leave her on place in analysis> | TBD |
| Tabular Microarray Panel | The numerical values of the expression measurements displayed in a table format; each row represents an individual probe and the columns display the signal and background intensities and intensity ratios. |
TBD |
Data Management
| Plugin | Description | Compatibility | Gene Panel | A subselection of markers which define data views by restricting number of markers shown. | TBD |
|---|---|---|---|---|---|
| Phenotype Panel | A subselection of microarrays which define data views by restricting number of arrays shown. | 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. | 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 | Normalization based on the average expression of all markers corresponding to user selected housekeeping genes. | TBD |
Annotation
| Plugin | Description | Compatibility |
|---|---|---|
| Dataset History | Lists data transformations induced by data-modifying operations. | ? |
| Dataset Annotation | A free text format box used by users to annotate data files, projects and images. | ? |
| Experiment Information | Displays any available experiment information associated with a Microarray dataset. | ? |
| Marker Annotation | Retrieves CGAP annotations for selected genes. | ? |
| caBIO Pathway Listing | Displays BioCarta pathway diagrams for selected genes. | TBD |
| Go Terms | Categorization of selected genes provided by the Gene Ontology Consortium (http://www.geneontology.org) displayed in a tree structure. | TBD |
Network Generation
| Plugin | Description | Compatibility |
|---|---|---|
| Reverse Engineering | Analyzes a large amount of microarray data (typically 100-500 microarrays) to reverse engineer the underlying gene regulatory network. | ? |
| 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) | An algorithm to perform clustering of real vectors defined on an instance space of dimensionality. | ? |
| T Test | The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform, made available from The Institute for Genomic Research (TIGR). | ? |
Sequence Analysis
| Plugin | Description | Compatibility |
|---|---|---|
| Synteny | A utility for comparison of extended genomic regions.- | ? |
Pattern Discovery
| Plugin | Description | Compatibility |
|---|---|---|
| Promoter Panel | - | ? |
| Sequence Panel | - | ? |
| Position Histogram | - | ? |
|- |}
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 |
