Difference between revisions of "Plugins"
Line 37: Line 37:
 
|-
 
|-
  
−
|SOM Clusters ||The Self Organizing Map (SOM) ||TBD
+
|SOM Clusters ||<''A should I leave her on place in analysis>'' ||TBD
 
|-
 
|-
 
|-
 
|-
Line 54: Line 54:
 
!Plugin||Description||Compatibility
 
!Plugin||Description||Compatibility
 
|-
 
|-
−
|Array-based centering||Subtracts the mean (median) measurement of a microarray from every measurement in that microarray.||TBD
+
|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
+
|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.
+
|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
 
||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.
+
|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
 
||TBD
 
|-
 
|-
Line 73: Line 73:
 
|-
 
|-
 
|-
 
|-
−
|Housekeeping ||The system is able to normalize data based on the values of user selected house-keeping genes.||TBD
+
|Housekeeping ||Normalization based on the average expression of all markers corresponding to user selected housekeeping genes.||TBD
 
|-
 
|-
  
Line 86: Line 86:
 
|-
 
|-
 
|-
 
|-
−
|Dataset Annotation||A text box used to annotate data files, projects and images.||?
+
|Dataset Annotation||A free text format  box used by users to annotate data files, projects and images.||?
 
|-
 
|-
 
|-
 
|-
−
|Experiment Information||This non-editable component allows for viewing experiment information associated with a Microarray dataset.||?
+
|Experiment Information||This non-editable component displays any available experiment information associated with a Microarray dataset .||?
−
|-
 
−
 
 
−
|-
 
−
|Image Annotation||Captures comments||?
 
 
|-
 
|-
 
|-
 
|-
Line 99: Line 95:
 
|-
 
|-
 
|-
 
|-
−
|CaBIO Pathway Listing||Displays BioCarta pathway diagrams for selected genes.||TBD--||?
+
|caBIO Pathway Listing||Displays BioCarta pathway diagrams for selected genes.||TBD
 
|-
 
|-
−
|Go Term||--||?
+
|Go Terms||Categorization of selected genes provided by the Gene Ontology Consortium (http://www.geneontology.org) displayed in a tree structure. ||TBD
 
|-
 
|-
 
|-
 
|-
Line 128: Line 124:
 
|-
 
|-
 
|Self Organizing Map (SOM)|| an algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||?
 
|Self Organizing Map (SOM)|| an algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||?
−
|-
 
 
|-
 
|-
 
|-
 
|-
Line 170: Line 165:
 
|-
 
|-
 
|-
 
|-
−
|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
+
|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
 
|-
 
|-
 
|-
 
|-
Line 176: Line 171:
 
|-
 
|-
 
|-
 
|-
−
|Expression threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
+
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
 
|-
 
|-
 
|-
 
|-
Line 183: Line 178:
  
 
|-
 
|-
−
|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
+
|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
+
|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
 
|-
 
|-
  

Revision as of 14:15, 31 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
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 are 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

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 This non-editable component records 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 This non-editable component 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
Retrieved from "http://wiki.c2b2.columbia.edu/workbench/index.php?title=Plugins&oldid=1726"