Difference between revisions of "Plugins"
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==Data Management==
 
==Data Management==
 
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!Plugin||Description
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!Plugin||Status||Description
 
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|width="150"|Marker Component ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.
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|width="150"|Marker Component ||Released||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.
 
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|width="150"|Phenotype/Array Component ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.
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|width="150"|Phenotype/Array Component ||Released||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.
 
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==Normalizers==
 
==Normalizers==
 
{|style="border: 1px solid lightGray"
 
{|style="border: 1px solid lightGray"
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!Plugin||Status||Description
 
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|width="150"|Array-Based Centering||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.
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.
+
|width="150"|Marker-Based Centering||Released||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.
 
|-
 
|-
 
|-
 
|-
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|width="150"|Mean-Variance Normalizer||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.
+
|width="150"|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.
 
|-
 
|-
 
|-
 
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|width="150"|Missing Value Calculation||Replacement of missing values with consensus values.
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|width="150"|Missing Value Calculation||Released||Replacement of missing values with consensus values.
 
|-
 
|-
 
|-
 
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|width="150"|Threshold Normalizer ||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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|width="150"|Quantile || 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 ||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"|Housekeeping || 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 ||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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{|style="border: 1px solid lightGray"
 
{|style="border: 1px solid lightGray"
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!Plugin||Description
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!Plugin||Status||Description
 
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|width="150"|Affy Detection Call||(''Affymetrix data only)'' Filtering of measurements based on the value of their "detection call" attribute.
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|width="150"|Affy Detection Call||Released||(''Affymetrix data only)'' Filtering of measurements based on the value of their "detection call" attribute.
 
|-
 
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|width="150"|Deviation|| Filtering of markers with low dynamic range.
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|width="150"|Deviation||Released|| Filtering of markers with low dynamic range.
 
|-
 
|-
 
|-
 
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|width="150"|Expression Threshold|| Elimination of measurements that fall outside a range of explression values.
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|width="150"|Expression Threshold||Released|| Elimination of measurements that fall outside a range of explression values.
 
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|width="150"|2-channel Threshold||(''Genepix data only)'' Same as "Expression Threshold" filter but different threshold ranges can be specified for each channel.
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|width="150"|2-channel Threshold||Released||(''Genepix data only)'' Same as "Expression Threshold" filter but different threshold ranges can be specified for each channel.
 
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|width="150"|Genepix Flag Filter|| ''(Genepix data only)'' Filtering of measurements based on the value of their "Flags" attribute.
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|width="150"|Genepix Flag Filter||Released|| ''(Genepix data only)'' Filtering of measurements based on the value of their "Flags" attribute.
 
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{|style="border: 1px solid lightGray"
 
{|style="border: 1px solid lightGray"
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!Plugin||Description
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!Plugin||Status||Description
 
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|width="150"|Dataset History||Log of data transformations induced by data-modifying operations.
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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||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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|-
 
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|width="150"|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed.
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|width="150"|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.
 
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|width="150"|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.  Includes visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]])..
+
|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||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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{|style="border: 1px solid lightGray"
 
{|style="border: 1px solid lightGray"
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!Plugin||Description
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!Plugin||Status||Description
 
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|width="150"|ARACNE|| 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"|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|| Extends ARACNE to include detecting the influence of modulators of transcription factor activity.
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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"|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 1.0]([[media:Cytoscape.png|screenshot]]).
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|width="150"|Cytoscape||Released||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 1.0]([[media:Cytoscape.png|screenshot]]).
 
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|width="150"|Cellular Networks Knowledge Base||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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{|style="border: 1px solid lightGray"
 
{|style="border: 1px solid lightGray"
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!Plugin||Status||Description
 
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|width="150"|Hierarchical Clustering||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"|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"|Self Organizing Map (SOM)|| 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"|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"|T-Test||Identification of markers with statistically significant differential expression between sets of microarrays. ([[media:Volcanoplot.png|screenshot]]).
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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"|ANOVA||Analysis of Variance - detection of significant differences in expression between more than two groups.
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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||Transcription Factor binding motifs.
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|width="150"|MRA||Released||Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis.
 
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|width="150"|PCA||(from GenePattern) Principal Component Analysis.
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|width="150"|MatrixReduce||Released||Transcription Factor binding motifs.
 
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|width="150"|Weighted Voting||(from GenePattern) Weighted Voting Analysis.
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|width="150"|PCA||Released||(from GenePattern) Principal Component Analysis.
 
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|width="150"|KNN||(from GenePattern) k-Nearest Neighbors analysis.
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|width="150"|Weighted Voting||Released||(from GenePattern) Weighted Voting Analysis.
 +
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 +
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|width="150"|KNN||Released||(from GenePattern) k-Nearest Neighbors analysis.
 
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== Sequence Analysis & Visualization ==
 
== Sequence Analysis & Visualization ==
 
{|style="border: 1px solid lightGray"
 
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|width="150"|Sequence Alignment||Run jobs on the NCBI BLAST servers directly within geWorkbench.  
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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"|Sequence Retriever||Retrieve sequences for annotated markers from Santa Cruz (nucleotide sequences) and EBI (proteins 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"|Synteny|| 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]]).
+
|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"|Promoter Analysis||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.]
+
|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"|Pattern  Discovery|| Discovery of sequence motifs in sets of DNA and protein sequences.
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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 || 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]]).  
+
|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 Panel || 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"|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 16:47, 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
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.
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).
CELImageViewer Released Visualization of data in Affymetrix CEL files.
ImageViewer Released Visualization of screenshots saved within geWorkbench (e.g. dendrograms).
Jmol Released Visualization of 3D protein structures from PDB files.
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.

Normalizers

Plugin Status Description
Array-Based Centering Released Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.
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 Calculation Released Replacement of missing values with consensus values.
Threshold Normalizer Released Adjustment of values that fall outside a user-specified threshold.
Quantile Released Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.
Housekeeping Released Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.

Filters

Plugin Status Description
Affy Detection Call Released (Affymetrix data only) Filtering of measurements based on the value of their "detection call" attribute.
Deviation 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.


Annotation

Plugin Status Description
Dataset History Released Log of data transformations induced by data-modifying operations.
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".
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.
Marker Annotations Released Retrieval of gene and pathway information for markers on a microarray. Includes visualization of BioCarta pathway diagrams (screenshot)..
Gene Ontology Released Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations (screenshot).

Network Generation

Plugin Status Description
ARACNe Released Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks (screenshot).
MINDy Released Extends ARACNe to include detecting the influence of modulators of transcription factor activity.
Cytoscape Released Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 1.0(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.

Analysis

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

Sequence Analysis & Visualization

Plugin Status Description
Sequence Alignment Released Run jobs on the NCBI BLAST servers directly within geWorkbench.
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).
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.
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).
Sequence Panel Released Visualization of results from the Pattern Discovery plugin, displaying the motif match location over each sequence from the input data set.
Retrieved from "http://wiki.c2b2.columbia.edu/workbench/index.php?title=Plugins&oldid=5905"