Difference between revisions of "Plugins"
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|width="150"|CELImageViewer ||Released  || Visualization of data in Affymetrix CEL files.
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|width="150"|Color Mosaic||Released  ||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).
 
|width="150"|Color Mosaic||Released  ||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).
 
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|width="150"|Dendrogram||Released  ||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).
 
|width="150"|Dendrogram||Released  ||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).
 
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|width="150"| ImageViewer ||Released|| Visualization of screenshots saved within geWorkbench (e.g. dendrograms).
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|width="150"| Jmol||Released  || Visualization of 3D protein structures from PDB files.
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|width="150"|Microarray Viewer||Released  ||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).
 
|width="150"|Microarray Viewer||Released  ||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).
 
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|width="150"|Scatter Plot ||Released  || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).
 
|width="150"|Scatter Plot ||Released  || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).
 
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|width="150"|SOM Clusters Viewer ||Released  ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]).   
 
|width="150"|SOM Clusters Viewer ||Released  ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]).   
 
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|width="150"|Tabular Microarray Viewer||Released  || Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:Tabular.png|screenshot]]).
 
|width="150"|Tabular Microarray Viewer||Released  || Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:Tabular.png|screenshot]]).
 
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|width="150"|CELImageViewer ||Released  || Visualization of data in Affymetrix CEL files.
 
 
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|width="150"| ImageViewer ||Released|| Visualization of screenshots saved within geWorkbench (e.g. dendrograms).
 
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|width="150"| Jmol||Released  || Visualization of 3D protein structures from PDB files.
 
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|width="150"| Volcano Plot||Released  || Visualize fold-change vs significance (P-value) for t-test results.
 
|width="150"| Volcano Plot||Released  || Visualize fold-change vs significance (P-value) for t-test results.
 
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{|style="border: 1px solid lightGray"
 
{|style="border: 1px solid lightGray"
 
!Plugin||Status||Description
 
!Plugin||Status||Description
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|width="150"|Array-Based Centering||Released||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.
 
|width="150"|Array-Based Centering||Released||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.
 
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|width="150"|Housekeeping ||Released|| Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.
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|width="150"|Housekeeping Normalizer||Released|| Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.
 
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|width="150"|Missing Value Calculation||Released||Replacement of missing values with consensus values.
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|width="150"|Missing Value Normalizer||Released||Replacement of missing values with consensus values.
 
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|width="150"|Quantile ||Released|| Expression measurements in each microarray are adjusted so that  the distribution of values is the same across all microarrays in an experiment.
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|width="150"|Quantile Normalizer||Released|| Expression measurements in each microarray are adjusted so that  the distribution of values is the same across all microarrays in an experiment.
 
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|width="150"|Threshold Normalizer ||Released||Adjustment of values that fall outside a user-specified threshold.
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|width="150"|Threshold Normalizer||Released||Adjustment of values that fall outside a user-specified threshold.
 
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!Plugin||Status||Description
 
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|width="150"|Dataset History||Released||Log of data transformations induced by data-modifying operations.
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|width="150"|Dataset Annotation||Released||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook.
 
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|width="150"|Dataset Annotation||Released||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".
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|width="150"|Dataset History||Released||Log of data transformations induced by data-modifying operations.
 
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|width="150"|Marker Annotations||Released||Retrieval of gene and pathway information for markers on a microarray. Includes visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]])..
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|width="150"|Gene Ontology||Released||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]).
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|width="150"|Gene Ontology||Released||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]).
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|width="150"|Marker Annotations||Released||Retrieval of gene and pathway information for markers on a microarray.  Includes visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).
 
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==Network Generation==
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==Network Generation, Networks==
  
 
{|style="border: 1px solid lightGray"
 
{|style="border: 1px solid lightGray"
 
!Plugin||Status||Description
 
!Plugin||Status||Description
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|width="150"|ARACNe||Released|| Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).
 
|width="150"|ARACNe||Released|| Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).
 
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|width="150"|MINDy||Released|| Extends ARACNe to include detecting the influence of modulators of transcription factor activity.
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|width="150"|Cellular Networks Knowledge Base||Released||Queries a local database housed at Columbia University which combines locally generated B-cell interaction network data with information from external databases.  Builds a network of interactions for selected genes.
 
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|width="150"|Cellular Networks Knowledge Base||Released||Queries a local database housed at Columbia University which combines locally generated B-cell interaction network data with information from external databases.  Builds a network of interactions for selected genes.
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|width="150"|MINDy||Released|| Extends ARACNe to include detecting the influence of modulators of transcription factor activity.
 
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!Plugin||Status||Description
 
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|width="150"|Hierarchical Clustering||Released||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.
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|width="150"|ANOVA||Released||Analysis of Variance - detection of significant differences in expression between more than two groups.
 
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|width="150"|Self Organizing Map (SOM)||Released|| Clustering of markers using self organizing maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.
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|width="150"|Hierarchical Clustering||Released||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.
 
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|width="150"|T-Test||Released||Identification of markers with statistically significant differential expression between sets of microarrays. ([[media:Volcanoplot.png|screenshot]]).
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|width="150"|KNN||Released||(from GenePattern) k-Nearest Neighbors analysis.
 
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|width="150"|ANOVA||Released||Analysis of Variance - detection of significant differences in expression between more than two groups.
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|width="150"|MatrixReduce||Released||Transcription Factor binding motifs.
 
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|width="150"|MatrixReduce||Released||Transcription Factor binding motifs.
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|width="150"|PCA||Released||(from GenePattern) Principal Component Analysis.
 
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|width="150"|PCA||Released||(from GenePattern) Principal Component Analysis.
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|width="150"|SOM||Released|| Clustering of markers using Self Organizing Maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.
 
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|width="150"|Weighted Voting||Released||(from GenePattern) Weighted Voting Analysis.
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|width="150"|T-Test||Released||Identification of markers with statistically significant differential expression between sets of microarrays. ([[media:Volcanoplot.png|screenshot]]).
 
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|width="150"|KNN||Released||(from GenePattern) k-Nearest Neighbors analysis.
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|width="150"|Weighted Voting||Released||(from GenePattern) Weighted Voting Analysis.
 
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|width="150"|Sequence Alignment||Released||Run jobs on the NCBI BLAST servers directly within geWorkbench.  
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|width="150"|Pattern  Discovery||Released|| Discovery of sequence motifs in sets of DNA and protein sequences.
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|width="150"|Position Histogram ||Released|| Visualization of results from the Pattern Discovery plugin. Motif/pattern support is plotted against relative sequence position of the motif match ([[media:Histogram.png|screenshot]]).
 
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|width="150"|Sequence Retriever||Released||Retrieve sequences for annotated markers from Santa Cruz (nucleotide sequences) and EBI (proteins sequences).
 
 
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|width="150"|Promoter Analysis||Released||Identification of putative transcription factor binding sites in DNA sequences ([[media:Promoterpanel.png|screenshot]]). The analysis use the profiles in the [http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl JASPAR Transcription Factor Binding Profile Database.]
 
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|width="150"|Synteny||Discontinued|| Comparison of sequence similarity between two genomic regions. The comparison results are represented as a dot matrix augmented with detailed annotation for both regions ([[media:Synteny Dotmatrix.png|screenshot]]).
 
 
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|width="150"|Sequence Alignment||Released||Run jobs on the NCBI BLAST servers directly within geWorkbench.
 
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|width="150"|Promoter Analysis||Released||Identification of putative transcription factor binding sites in DNA sequences ([[media:Promoterpanel.png|screenshot]]). The analysis use the profiles in the [http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl JASPAR Transcription Factor Binding Profile Database.]
 
 
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|width="150"|Sequence Panel ||Released|| Visualization of results from the Pattern Discovery plugin, displaying the motif match location over each sequence from the input data set.
 
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|width="150"|Pattern  Discovery||Released|| Discovery of sequence motifs in sets of DNA and protein sequences.
 
 
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|width="150"|Sequence Retriever||Released||Retrieve sequences for annotated markers from Santa Cruz (nucleotide sequences) and EBI (proteins sequences).
 
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|width="150"|Position Histogram ||Released|| Visualization of results from the Pattern Discovery plugin. Motif/pattern support is plotted against relative sequence position of the motif match ([[media:Histogram.png|screenshot]]).
 
 
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|width="150"|Synteny||Discontinued|| Comparison of sequence similarity between two genomic regions. The comparison results are represented as a dot matrix augmented with detailed annotation for both regions ([[media:Synteny Dotmatrix.png|screenshot]]).
 
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|width="150"|Sequence Panel ||Released|| Visualization of results from the Pattern Discovery plugin, displaying the motif match location over each sequence from the input data set.
 
 
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Revision as of 18:07, 11 February 2010

The geWorkbench platform employs a component repository infrastructure to manage a large collection of pluggable components that can be used to customize the application's graphical user interface. This (ever growing) list of plug-in components covers a wide range of fucntionality for a number of different genomic data modalities.



Visualization

Plugin Status Description
CELImageViewer Released Visualization of data in Affymetrix CEL files.
Color Mosaic Released Heat maps for microarray expression data, organized by phenotypic or gene groupings (screenshot).
Dendrogram Released Tree-structured diagrams reflecting the results of hierarchical clustering analysis (screenshot).
Expression Profiles Released Line graph of genes expression profiles across several arrays/ hybridizations (screenshot).
Expression Value Distribution Released Distribution plot of marker expression values across one or more microarrays.
ImageViewer Released Visualization of screenshots saved within geWorkbench (e.g. dendrograms).
Jmol Released Visualization of 3D protein structures from PDB files.
Microarray Viewer Released Color-gradient representation of gene expression values (screenshot).
Scatter Plot Released Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values (screenshot).
SOM Clusters Viewer Released Visualization of gene clusters produced by the self-organizing maps analysis (screenshot).
Tabular Microarray Viewer Released Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray (screenshot).
Volcano Plot Released Visualize fold-change vs significance (P-value) for t-test results.


Data Management

Plugin Status Description
Marker Component Released Definition of data views consisting of marker subgroups. The views control the amount of data displayed.
Phenotype/Array Component Released Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.
Project Component Released Manages projects and workspaces of the user.


Normalization

Plugin Status Description
Array-Based Centering Released Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.
Housekeeping Normalizer Released Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.
Log2 Normalizer Released The log2 transformation is applied to all measurements in a microarray, if all values in all microarrays are positive.
Marker-Based Centering Released Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.
Mean-Variance Normalizer Released Transformation of expression measurements to standard units: for every marker, the mean measurement of the marker profile (across all microarrays in an experiment) is subtracted from each measurement in the profile and the resulting value is divided by the standard deviation of the profile.
Missing Value Normalizer Released Replacement of missing values with consensus values.
Quantile Normalizer Released Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.
Threshold Normalizer Released Adjustment of values that fall outside a user-specified threshold.


Filtering

Plugin Status Description
Affy Detection Call Released (Affymetrix data only) Filtering of measurements based on the value of their "detection call" attribute.
Deviation Filter Released Filtering of markers with low dynamic range.
Expression Threshold Released Elimination of measurements that fall outside a range of explression values.
2-channel Threshold Released (Genepix data only) Same as "Expression Threshold" filter but different threshold ranges can be specified for each channel.
Genepix Flag Filter Released (Genepix data only) Filtering of measurements based on the value of their "Flags" attribute.
Missing Value Filter Released Discards all markers that have missing measurements in more than a user specified number N of microarrays.


Annotation

Plugin Status Description
Dataset Annotation Released Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook.
Dataset History Released Log of data transformations induced by data-modifying operations.
Experiment Information Released Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed.
Gene Ontology Released Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations (screenshot).
Marker Annotations Released Retrieval of gene and pathway information for markers on a microarray. Includes visualization of BioCarta pathway diagrams (screenshot).


Network Generation, Networks

Plugin Status Description
ARACNe Released Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks (screenshot).
Cellular Networks Knowledge Base Released Queries a local database housed at Columbia University which combines locally generated B-cell interaction network data with information from external databases. Builds a network of interactions for selected genes.
Cytoscape Released Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 1.0(screenshot).
MINDy Released Extends ARACNe to include detecting the influence of modulators of transcription factor activity.


Analysis

Plugin Status Description
ANOVA Released Analysis of Variance - detection of significant differences in expression between more than two groups.
Hierarchical Clustering Released Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.
KNN Released (from GenePattern) k-Nearest Neighbors analysis.
MatrixReduce Released Transcription Factor binding motifs.
MRA Released Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis.
PCA Released (from GenePattern) Principal Component Analysis.
SOM Released Clustering of markers using Self Organizing Maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.
T-Test Released Identification of markers with statistically significant differential expression between sets of microarrays. (screenshot).
Weighted Voting Released (from GenePattern) Weighted Voting Analysis.


Sequence Analysis & Visualization

Plugin Status Description
Pattern Discovery Released Discovery of sequence motifs in sets of DNA and protein sequences.
Position Histogram Released Visualization of results from the Pattern Discovery plugin. Motif/pattern support is plotted against relative sequence position of the motif match (screenshot).
Promoter Analysis Released Identification of putative transcription factor binding sites in DNA sequences (screenshot). The analysis use the profiles in the JASPAR Transcription Factor Binding Profile Database.
Sequence Alignment Released Run jobs on the NCBI BLAST servers directly within geWorkbench.
Sequence Panel Released Visualization of results from the Pattern Discovery plugin, displaying the motif match location over each sequence from the input data set.
Sequence Retriever Released Retrieve sequences for annotated markers from Santa Cruz (nucleotide sequences) and EBI (proteins sequences).
Synteny Discontinued Comparison of sequence similarity between two genomic regions. The comparison results are represented as a dot matrix augmented with detailed annotation for both regions (screenshot).
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