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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.

The Status of the pluggable components below is defined as:


StatusComment
(a) ReleasedThis plugin is part of the latest geWorkbench version.
(b) DevelopmentThis plugin is currently actively being developed.


Contents


Analysis

PluginStatusDescription
ANOVAReleasedAnalysis of Variance - detection of significant differences in expression between more than two groups. (Screenshot)
Evidence IntegrationDevelopmentA sequence and structure-based approach for functional annotation and protein-protein interaction analysis.
GSEAReleasedThe Gene Set Enrichment Analysis determines whether an a priori defined set of genes shows statistically significant differences between two phenotypes.
Hierarchical ClusteringReleasedClustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin. (Screenshot)
KNNReleasedk-Nearest Neighbors analysis (a GenePattern component).
MatrixReduceReleasedTranscription Factor binding motifs. (Screenshot)
MEDUSADevelopmentThe Motif Element Detection Using Sequence Agglomeration is an integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data (Leslie Lab, MSKCC).
MRAReleasedMaster Regulator Analysis combines regulatory information from interaction networks with differential expression analysis. (Screenshot)
PCAReleasedPrincipal Component Analysis (a GenePattern component).
SOMReleasedClustering of markers using Self Organizing Maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin. (Screenshot)
SVM 3.0ReleasedThe Support Vector Machine is a supervised classification method that computes a maximal separating hyperplane between the expression vectors of different classes or phenotypes (a GenePattern component).
T-TestReleasedIdentification of markers with statistically significant differential expression between sets of microarrays. (Screenshot Plot, Screenshot Mosaic)
Weighted VotingReleasedWeighted Voting Analysis (a GenePattern component).


Annotation

PluginStatusDescription
caScriptDevelopmentAn Editor.
Dataset HistoryReleasedLog of data transformations induced by data-modifying operations.
Experiment InformationReleasedMicroarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed.
Gene Ontology EnrichmentReleasedEnrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations. (Screenshot)
Marker AnnotationsReleasedRetrieval of gene and pathway information for markers on a microarray (caBIO Pathways/Cancer Gene Index); it includes visualization of BioCarta pathway diagrams. (Screenshot Table, Screenshot BioCarta, Screenshot CGI)


Data Filtering

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


Data Management

PluginStatusDescription
Arrays/PhenotypesReleasedDefinition of data views consisting of microarray subgroups. The views control the amount of data displayed. (Screenshot)
caArrayReleasedSearch and download of gene expression data from instances of caArray (NCI microarray database product). (Screenshot)
MarkersReleasedDefinition of data views consisting of marker subgroups. The views control the amount of data displayed. (Screenshot)
Project FoldersReleasedManages projects and workspaces of the user. (Screenshot)


File Import

PluginStatusDescription
Affymetrix CELReleasedLoads Affymetrix probe CELl intensity files ("*.cel").
Affymetrix File MatrixReleased Loads Affymetrix EXPperiment files ("*.exp").
Affymetrix MAS5/GCOSReleased Loads output files from the GeneChip Operating Software formerly known as MAS5 Statistical algorithm (several different file extension).
FASTA FormatReleasedLoads files that are in FASTA format ("*.fasta" and "*.txt").
Genepix File FormatReleasedLoads files in GenePix Result format ("*.gpr").
PDB Structure FormatReleasedLoads files in the Protein Data Base format ("*.pdb")
Tab-delimited (RMA Express Format)ReleasedLoads tab-delimited files from the Robust Multichip Analysis ("*.txt")


Menu Tools

PluginStatusDescription
CCMReleasedThe Component Configuration Manager allows users to manage plugins dynamically at any given time in the application environment. (Screenshot)
genSpaceReleasedIt logs information about the analysis tools used in geWorkbench in order to enable collaboration support for the geWorkbench users.
Online HelpReleasedgeWorkbench Online Help uses the Java help 2.0 system to provide real-time help on component questions.
PreferencesReleasedAllows users to predefine a few basic visual settings and choose a Text Editor.
Version InformationReleasedProvides basic information about the currently installed user version of geWorkbench.
Welcome ScreenReleasedIntroduction to geWorkbench during the initial opening of the application.


Network Generation

PluginStatusDescription
ARACNeReleasedThe Algorithm for the Reconstruction of Accurate Cellular Networks analyses large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks. (Screenshot)
Cancer GEMSDevelopmentInterface to the NCI Cancer Genetic Markers of Susceptibility project.
CNKBReleasedThe Cellular Networks Knowledge Base queries an in-house repository of locally generated B-cell interaction network data and information from external databases in order to build a network of interactions for selected genes. (Screenshot Throttle Graph, Screenshot Network)
CytoscapeReleasedVisualization of gene regulatory network created in Reverse Engineering using Cytoscape 1.0. (Screenshot)
MINDyReleasedThe Modulator Inference by Network Dynamics algorithm extends ARACNe to include detecting the influence of modulators of transcription factor activity.
NetBoostDevelopmentNetBoost is a network characterization algorithm.


Normalization

PluginStatusDescription
Array-Based CenteringReleasedSubtraction of the mean or median measurement of a microarray from every measurement in that microarray.
Housekeeping NormalizerReleased Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.
Log2 NormalizerReleasedApplies a log2 transformation to all measurements in a microarray.
Marker-Based CenteringReleasedSubtraction of the mean or median measurement of a marker profile from every measurement in the profile.
Mean-Variance NormalizerReleasedTransformation 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 NormalizerReleasedReplacement of missing values with consensus values.
Quantile NormalizerReleased Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.
Threshold NormalizerReleasedAdjustment of values that fall outside a user-specified threshold.


Protein Structure Analysis

PluginStatusDescription
MarkUsReleasedAssesses the biochemical function for a given protein structure. (Screenshot)
PudgeReleasedComputational protein structure prediction using sequence homology. It integrates tools used at different stages of the structural prediction process. (Screenshot Parameters, Screenshot Result)
SkyBaseReleasedDatabase of protein structure models produced by SkyLine based on structures solved by the NESG structural genomics consortium.
SkyLineReleasedAutomated high-throughput pipeline for reverse homology-based comparative protein structure modeling based on the input template structure.


Sequence Analysis & Visualization

PluginStatusDescription
Alignment ResultsReleasedIt parses and displays the results of sequence similarity searches which were run on the NCBI BLAST service. (Screenshot)
Pattern DiscoveryReleased Discovery of sequence motifs in sets of DNA and protein sequences. (Screenshot)
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 AnalysisReleasedIdentification of putative transcription factor binding sites in DNA sequences. The analysis use the profiles in the JASPAR Transcription Factor Binding Profile Database. (Screenshot Logo, Screenshot Sequence 1, Screenshot Sequence 2)
Sequence AlignmentReleasedRun 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 RetrieverReleasedRetrieve sequences for annotated markers from Santa Cruz (Nucleotides) and EBI (Proteins). (Screenshot)


Visualization

PluginStatusDescription
Analysis PanelReleasedFramework to support numerous, individually loadable analysis methods.
ANOVA Tabular ViewerReleasedDisplays the results of ANOVA analysis of gene expression data in tabular format. (Screenshot)
CEL Image ViewerReleasedVisualization of data in Affymetrix CEL files. (Screenshot)
Color MosaicReleasedHeat maps for microarray expression data, organized by phenotypic or gene groupings. (Screenshot)
DendrogramReleasedTree-structured diagrams reflecting the results of hierarchical clustering analysis. (Screenshot)
Evidence Integration ViewerDevelopmentDisplays the results of the Evidence Integration analysis.
Expression ProfilesReleasedLine graph of genes expression profiles across several arrays/ hybridizations. (Screenshot)
Expression Value DistributionReleasedDistribution plot of marker expression values across one or more microarrays. (Screenshot)
GeneWaysReleasedAn essential component needed to display elements in Cytoscape and ARACNe.
GO Terms ViewerReleasedDisplays the results of Gene Ontology Enrichment Analysis. (Screenshot)
Image ViewerReleasedVisualization of screenshots saved within geWorkbench (e.g. dendrograms).
JmolReleased Visualization of 3D protein structures from PDB files. (Screenshot)
Mark-Us BrowserReleased Displays the results of a Mark-Us analysis. (Screenshot)
MatrixReduceReleasedVisualization of MatrixReduce calculations using logo, chromosomal and tabular displays.
MEDUSA ViewerDevelopmentDisplays the results of a MEDUSA analysis.
Microarray ViewerReleasedColor-gradient representation of gene expression values. (Screenshot)
MINDy ViewerReleasedThe results of a MINDy calculation are presented in several different tabular displays and a heat map.
MRA ViewerReleasedDisplays the results of the MRA in tablular and graphical form. (Screenshot)
NetBoost ViewerDevelopmentDisplays a Boosting Iteration Graph, Confusion Matrix and Score Table from NetBoost Analysis.
Normalization PanelReleasedFramework to support numerous, individually loadable normalization components.
PCA ViewerReleasedDisplays PCA results.
Pudge BrowserReleasedVisualization of Pudge results. (Screenshot Parameters, Screenshot Result)
Scatter PlotReleasedPairwise (array vs. array and marker vs. marker) comparison and plotting of expression values. (Screenshot Array, Screenshot Marker)
SkyBase ViewerReleasedDisplays the results from the SkyBase search.
SkyLine Output AllReleasedDisplays all models from the Skyline modeling.
SkyLine Output EachReleasedDisplays each model from the Skyline modeling.
SkyLine ContourDevelopmentA 2D dominance-based visualization of query results.
SOM Clusters ViewerReleasedVisualization of gene clusters produced by the self-organizing maps analysis. (Screenshot)
SVM ViewerReleasedVisualizes results obtained from classifying samples based on SVMs generated using the Gene Pattern v3 SVM service.
Tabular Microarray ViewerReleasedSpreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray. (Screenshot)
Volcano PlotReleased Visualize fold-change vs significance (P-value) for t-test results. (Screenshot)
  • This page was last modified on 16 July 2013, at 15:17.
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