Difference between revisions of "Plugins"
 
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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 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:
 +
 +
 +
{|style="border: 1px solid lightGray"
 +
!Status||Comment
 +
|-
 +
|-
 +
|width="120"|(a) Released||This plugin is part of the latest geWorkbench version.
 +
|-
 +
|width="120"|(b) Development||This plugin is currently actively being developed.
 +
|-
 +
|-
 +
|}
  
  
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−
==Visualization==
+
==Analysis==
  
−
{|style="border: 1px solid lightGray"
+
{|class = "wikitable" style="border: 1px solid lightGray"
 
!Plugin||Status||Description
 
!Plugin||Status||Description
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Analysis Panel||Released ||Framework to support numerous, individually loadable analysis methods.
+
|width="150"|ANOVA||Released||Analysis of Variance - detection of significant differences in expression between more than two groups. ([[media:T_ANOVA_ColorMosaic.png|Screenshot]])
 +
|-
 +
|-
 +
|width="150"|Evidence Integration||Development||A sequence and structure-based approach for functional annotation and protein-protein interaction analysis.
 +
|-
 
|-
 
|-
 +
|width="150"|GSEA||Released||The Gene Set Enrichment Analysis determines whether an a priori defined set of genes shows statistically significant differences between two phenotypes.
 
|-
 
|-
−
|width="150"|ANOVA Tabular Viewer||Released||Displays the results of ANOVA analysis of gene expression  data in tabular format.
 
 
|-
 
|-
 +
|width="150"|Hierarchical Clustering||Released||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin. ([[media:T_HC_Dendrogram_display.png|Screenshot]])
 
|-
 
|-
−
|width="150"|CELImageViewer||Released||Visualization of data in Affymetrix CEL files.
 
 
|-
 
|-
 +
|width="150"|KNN||Released||k-Nearest Neighbors analysis (a GenePattern component).
 +
|-
 +
|-
 +
|width="150"|MatrixReduce||Released||Transcription Factor binding motifs. ([[media:T_MatrixREDUCE_PSAM_view.png|Screenshot]])
 +
|-
 +
|-
 +
|width="150"|MEDUSA||Development||The 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).
 +
|-
 +
|-
 +
|width="150"|MRA||Released||Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis. ([[media:MRA_viewer_full.png|Screenshot]])
 +
|-
 +
|-
 +
|width="150"|PCA||Released||Principal Component Analysis (a GenePattern component).
 
|-
 
|-
−
|width="150"|Color Mosaic||Released||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).
+
|-
 +
|width="150"|SOM||Released||Clustering of markers using Self Organizing Maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin. ([[media:T_SOM_result.png|Screenshot]])
 +
|-
 +
|-
 +
|width="150"|SVM 3.0||Released||The 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).
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Dendrogram||Released||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).
+
|width="150"|T-Test||Released||Identification of markers with statistically significant differential expression between sets of microarrays. ([[media:T_t-test_volcano_BCELL_webm_qldm.png|Screenshot Plot]], [[media:T_t-test_colormosaic_BCELL_webm_qldm.png|Screenshot Mosaic]])
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Evidence Integration Viewer||Development||Displays the results of the Evidence Integration analysis.
+
|width="150"|Weighted Voting||Released||Weighted Voting Analysis (a GenePattern component).
−
|-
+
|-
 +
|-
 +
|}
 +
 
 +
 
 +
==Annotation==
 +
 
 +
{|class = "wikitable" style="border: 1px solid lightGray"
 +
!Plugin||Status||Description
 
|-
 
|-
−
|width="150"|Expression Profiles||Released||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).
 
−
|-
 
 
|-
 
|-
−
|width="150"|Expression Value Distribution||Released||Distribution plot of marker expression values across one or more microarrays.
+
|width="150"|caScript||Development||An Editor.
 
|-
 
|-
 +
|-|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 notebook.
 
|-
 
|-
−
|width="150"|GO Terms Viewer||Released||Displays the results of Gene Ontology Enrichment Analysis.
 
−
|-
 
−
|-
 
−
|width="150"|Image Viewer||Released||Visualization of screenshots saved within geWorkbench (e.g. dendrograms).
 
−
|-
 
−
|-
 
−
|width="150"|Jmol||Released || Visualization of 3D protein structures from PDB files.
 
−
|-
 
 
|-
 
|-
−
|width="150"|Mark-Us Browser||Released || Displays the results of a MarkUs analysis.
+
|width="150"|Dataset History||Released||Log of data transformations induced by data-modifying operations.
−
|-
 
 
|-
 
|-
−
|width="150"|MatrixReduce||Released||Visualization of MatrixReduce calculations using logo, chromosomal and tabular displays.
 
−
|-
 
 
|-
 
|-
−
|width="150"|MEDUSA Viewer||Development||Displays the results of a MEDUSA analysis.
+
|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.
−
|-
 
 
|-
 
|-
−
|width="150"|Microarray Viewer||Released||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).
 
−
|-
 
 
|-
 
|-
−
|width="150"|MINDy Viewer||Released||The results of a MINDy calculation are presented in several different tabular displays and a heat map.
+
|width="150"|Gene Ontology Enrichment||Released||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations. ([[media:T_GO_Terms_TableBrowser_Gene_Detail.png|Screenshot]])
−
|-
 
 
|-
 
|-
−
|width="150"|MRA Viewer||Released||Displays the results of the MRA in tablular and graphical form.
 
−
|-
 
 
|-
 
|-
−
|width="150"|NetBoost Viewer||Development||Displays a Boosting Iteration Graph, Confusion Matrix and Score Table from NetBoost Analysis.
+
|width="150"|Marker Annotations||Released||Retrieval of gene and pathway information for markers on a microarray (caBIO Pathways/Cancer Gene Index); it includes visualization of BioCarta pathway diagrams. ([[media:GeWB_Marker_Annotations.png|Screenshot Table]], [[media:GeWB_Marker_Annotations_Pathway.png|Screenshot BioCarta]], [[media:GeWB_Marker_Annotations_CGI.png|Screenshot CGI]])
−
|-
 
 
|-
 
|-
−
|width="150"|Normalization Panel||Released ||Framework to support numerous, individually loadable normalization components.
 
 
|-
 
|-
 +
|}
 +
 +
 +
==Data Filtering==
 +
 +
{|class = "wikitable" style="border: 1px solid lightGray"
 +
!Plugin||Status||Description
 
|-
 
|-
−
|width="150"|PCA Viewer||Released ||Displays PCA results.
 
 
|-
 
|-
 +
|width="150"|Affy Detection Call Filter||Released||Filtering of measurements based on the value of their "detection call" attribute ''(Affymetrix data only)'' .
 
|-
 
|-
−
|width="150"|Pudge Browser||Released ||Visualization of Pudge results.
 
−
|-
 
 
|-
 
|-
−
|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"|Deviation Filter||Released||Filtering of markers with low dynamic range.
−
|-
 
 
|-
 
|-
−
|width="150"|SkyBase Viewer||Development||
 
−
|-
 
 
|-
 
|-
−
|width="150"|SkyLine Output All||Development||Displays all models from the Skyline modeling.
+
|width="150"|Expression Threshold Filter||Released||Elimination of measurements that fall outside a range of explression values.
−
|-
 
 
|-
 
|-
−
|width="150"|SkyLine Output Each||Development||Displays each model from the Skyline modeling.
 
−
|-
 
 
|-
 
|-
−
|width="150"|SOM Clusters Viewer||Released||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]).
+
|width="150"|2-channel Threshold Filter||Released||Same as "Expression Threshold" filter but different threshold ranges can be specified for each channel ''(GenePix data only)''.
 
|-
 
|-
 
|-
 
|-
−
|width="150"|SVM Viewer||Released||Visualizes results obtained from classifying samples based on SVMs generated using the Gene Pattern v3 SVM service.  
+
|width="150"|Genepix Flag Filter||Released||Filtering of measurements based on the value of their "Flags" attribute ''(GenePix data only)''.
−
|-
 
 
|-
 
|-
−
|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"|Missing Value Filter||Released||Discards all markers that have missing  measurements in more than a user specified number N of microarrays.
 
|-
 
|-
−
|width="150"| Volcano Plot||Released  || Visualize fold-change vs significance (P-value) for t-test results.
 
−
|-
 
 
|-
 
|-
 
|}
 
|}
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==Data Management==
 
==Data Management==
  
−
{|style="border: 1px solid lightGray"
+
{|class = "wikitable" style="border: 1px solid lightGray"
 
!Plugin||Status||Description
 
!Plugin||Status||Description
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Marker Component ||Released||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.
+
|width="150"|Arrays/Phenotypes||Released||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed. ([[media:T_t-test_Arrays_case-set_BCELL_webm_qldm.png|Screenshot]])
−
|-
+
|-
 +
|-
 +
|width="150"|caArray||Released||Search and download of gene expression data from instances of caArray (NCI microarray database product). ([[media:T_caArray_A549_arrays.png|Screenshot]])
 
|-
 
|-
−
|width="150"|Phenotype/Array Component ||Released||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.
 
 
|-
 
|-
 +
|width="150"|Markers||Released||Definition of data views consisting of marker subgroups. The views control the amount of data displayed. ([[media:Select_marker_sets.png|Screenshot]])
 +
|-
 
|-
 
|-
−
|width="150"|Project Component ||Released||Manages projects and workspaces of the user.
+
|width="150"|Project Folders||Released||Manages projects and workspaces of the user. ([[media:T_ANOVA_Saved_Color_Mosaic_View.png|Screenshot]])
 
|-
 
|-
 
|-
 
|-
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−
==Normalization==
+
==File Import==
  
−
{|style="border: 1px solid lightGray"
+
{|class = "wikitable" style="border: 1px solid lightGray"
 
!Plugin||Status||Description
 
!Plugin||Status||Description
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Array-Based Centering||Released||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.
+
|width="150"|Affymetrix CEL||Released||Loads Affymetrix probe CELl intensity files ("*.cel").
−
|-
 
 
|-
 
|-
−
|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.
 
 
|-
 
|-
 +
|width="150"|Affymetrix File Matrix||Released|| Loads Affymetrix EXPperiment files ("*.exp").
 
|-
 
|-
−
|width="150"|Log2 Normalizer||Released||The log2 transformation is applied to all measurements in a microarray, if all values in all microarrays are positive.
 
 
|-
 
|-
 +
|width="150"|Affymetrix MAS5/GCOS||Released|| Loads output files from the GeneChip Operating Software formerly known as MAS5 Statistical algorithm (several different file extension).
 
|-
 
|-
−
|width="150"|Marker-Based Centering||Released||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.
 
 
|-
 
|-
 +
|width="150"|FASTA Format||Released||Loads files that are in FASTA format ("*.fasta" and "*.txt").
 
|-
 
|-
−
|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.
 
 
|-
 
|-
 +
|width="150"|Genepix File Format||Released||Loads files in GenePix Result format ("*.gpr").
 
|-
 
|-
−
|width="150"|Missing Value Normalizer||Released||Replacement of missing values with consensus values.
 
 
|-
 
|-
 +
|width="150"|PDB Structure Format||Released||Loads files in the Protein Data Base format ("*.pdb")
 
|-
 
|-
−
|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.
 
 
|-
 
|-
−
|-
+
|width="150"|Tab-delimited (RMA Express Format)||Released||Loads tab-delimited files from the Robust Multichip Analysis ("*.txt")
−
|width="150"|Threshold Normalizer||Released||Adjustment of values that fall outside a user-specified threshold.
 
 
|-
 
|-
 
|-
 
|-
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−
==Filtering==
+
==Menu Tools==
  
−
{|style="border: 1px solid lightGray"
+
{|class = "wikitable" style="border: 1px solid lightGray"
 
!Plugin||Status||Description
 
!Plugin||Status||Description
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Affy Detection Call||Released||(''Affymetrix data only)'' Filtering of measurements based on the value of their "detection call" attribute.
+
|width="150"|CCM||Released||The Component Configuration Manager allows users to manage plugins dynamically at any given time in the application environment. ([[Media:CCM_Main.png|Screenshot]])
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Deviation Filter||Released|| Filtering of markers with low dynamic range.
+
|width="150"|genSpace||Released||It logs information about the analysis tools used in geWorkbench in order to enable collaboration support for the geWorkbench users.
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Expression Threshold||Released|| Elimination of measurements that fall outside a range of explression values.
+
|width="150"|Online Help||Released||geWorkbench Online Help uses the Java help 2.0 system to provide real-time help on component questions.
 
|-
 
|-
 
|-
 
|-
−
|width="150"|2-channel Threshold||Released||(''Genepix data only)'' Same as "Expression Threshold" filter but different threshold ranges can be specified for each channel.
+
|width="150"|Preferences||Released||Allows users to predefine a few basic visual settings and choose a Text Editor.
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Genepix Flag Filter||Released|| ''(Genepix data only)'' Filtering of measurements based on the value of their "Flags" attribute.
+
|width="150"|Version Information||Released||Provides basic information about the currently installed user version of geWorkbench.
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Missing Value Filter||Released|| Discards all markers that have missing  measurements in more than a user specified number N of microarrays.
+
|width="150"|Welcome Screen||Released||Introduction to geWorkbench during the initial opening of the application.
 
|-
 
|-
 
|-
 
|-
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−
==Annotation==
+
==Network Generation==
  
−
{|style="border: 1px solid lightGray"
+
{|class = "wikitable" style="border: 1px solid lightGray"
 
!Plugin||Status||Description
 
!Plugin||Status||Description
 
|-
 
|-
 
|-
 
|-
−
|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.
+
|width="150"|ARACNe||Released||The 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. ([[media:T_ARACNE_result1.png|Screenshot]])
 +
|-
 
|-
 
|-
 +
|width="150"|Cancer GEMS||Development||Interface to the NCI Cancer Genetic Markers of Susceptibility project.
 
|-
 
|-
−
|width="150"|Dataset History||Released||Log of data transformations induced by data-modifying operations.
 
 
|-
 
|-
 +
|width="150"|CNKB||Released||The 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. ([[media:T_CNKB_ProtDNA_confidence75.png|Screenshot Throttle Graph]], [[media:T_CNKB_10at75_Cytoscape.png|Screenshot Network]])
 
|-
 
|-
−
|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.
 
 
|-
 
|-
 +
|width="150"|Cytoscape||Released||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 1.0]. ([[media:T_ARACNE_result1.png|Screenshot]])
 
|-
 
|-
−
|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]]).
 
 
|-
 
|-
 +
|width="150"|MINDy||Released||The Modulator Inference by Network Dynamics algorithm extends ARACNe to include detecting the influence of modulators of transcription factor activity.
 
|-
 
|-
−
|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]]).
 
 
|-
 
|-
 +
|width="150"|NetBoost||Development||NetBoost is a network characterization algorithm.
 
|-
 
|-
 
|}
 
|}
  
  
−
==Network Generation, Networking==
+
==Normalization==
  
−
{|style="border: 1px solid lightGray"
+
{|class = "wikitable" style="border: 1px solid lightGray"
 
!Plugin||Status||Description
 
!Plugin||Status||Description
 
|-
 
|-
 
|-
 
|-
−
|width="150"|ARACNe||Released||The 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 ([[media:Reverseengineering.png|screenshot]]).
+
|width="150"|Array-Based Centering||Released||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.
 +
|-
 
|-
 
|-
 +
|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.
 
|-
 
|-
−
|width="150"|caArray||Released||Search and download of gene expression data from instances of caArray (NCI microarray database product).
 
 
|-
 
|-
 +
|width="150"|Log2 Normalizer||Released||Applies a log2 transformation to all measurements in a microarray.
 +
|-
 +
|-
 +
|width="150"|Marker-Based Centering||Released||Subtraction of the mean or median measurement of a marker profile from every measurement in 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.
 +
|-
 +
|-
 +
|width="150"|Missing Value Normalizer||Released||Replacement of missing values with consensus values.
 +
|-
 +
|-
 +
|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.
 
|-
 
|-
−
|width="150"|Cancer GEMS||Development||Interface to the NCI Cancer Genetic Markers of Susceptibility project.
 
 
|-
 
|-
 +
|width="150"|Threshold Normalizer||Released||Adjustment of values that fall outside a user-specified threshold.
 
|-
 
|-
−
|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.
 
 
|-
 
|-
 +
|}
 +
 +
 +
== Protein Structure Analysis ==
 +
 +
{|class = "wikitable" style="border: 1px solid lightGray"
 +
!Plugin||Status||Description
 
|-
 
|-
−
|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]]).
 
 
|-
 
|-
 +
|width="150"|MarkUs||Released||Assesses the biochemical function for a given protein structure. ([[media:T_MarkUs_Web_result.png|Screenshot]])
 
|-
 
|-
−
|width="150"|genSpace||Released||It logs information about the analysis tools that geWorkbench users run, so as to answer such questions as "what are the most commonly used analysis tools?" or "which analysis tools are most commonly used together?".
 
 
|-
 
|-
 +
|width="150"|Pudge||Released||Computational protein structure prediction using sequence homology. It integrates tools used at different stages of the structural prediction process. ([[media:T_Pudge_Parameters.png|Screenshot Parameters]], [[media:T_Pudge_Alignment_example.png|Screenshot Result]])
 
|-
 
|-
−
|width="150"|MINDy||Released||The Modulator Inference by Network Dynamics algorithm extends ARACNe to include detecting the influence of modulators of transcription factor activity.
+
|-
 +
|width="150"|SkyBase||Released||Database of protein structure models produced by SkyLine based on structures solved by the NESG structural genomics consortium.
 
|-
 
|-
 
|-
 
|-
−
|width="150"|NetBoost||Development||NetBoost is a network characterization algorithm.
+
|width="150"|SkyLine||Released||Automated high-throughput pipeline for reverse homology-based comparative protein structure modeling based on the input template structure.
 
|-
 
|-
 
|-
 
|-
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−
==Analysis==
+
== Sequence Analysis & Visualization ==
  
−
{|style="border: 1px solid lightGray"
+
{|class = "wikitable" style="border: 1px solid lightGray"
 
!Plugin||Status||Description
 
!Plugin||Status||Description
 
|-
 
|-
 
|-
 
|-
−
|width="150"|ANOVA||Released||Analysis of Variance - detection of significant differences in expression between more than two groups.
+
|width="150"|Alignment Results||Released||It parses and displays the results of sequence similarity searches which were run on the NCBI BLAST service. ([[media:T_SequenceAlignment_BLAST_results.png|Screenshot]])
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Evidence Integration||Development||
+
|width="150"|Pattern  Discovery||Released|| Discovery of sequence motifs in sets of DNA and protein sequences. ([[media:T_PatternDiscovery_Params_Basic_histone_result_exact_seqs.png|Screenshot]])
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Hierarchical Clustering||Released||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.
+
|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:T_PatternDiscovery_Histones_Result_exact_Position_Histogram.png|Screenshot]])
 
|-
 
|-
 
|-
 
|-
−
|width="150"|KNN||Released||k-Nearest Neighbors analysis (from GenePattern).
+
|width="150"|Promoter Analysis||Released||Identification of putative transcription factor binding sites in DNA sequences. The analysis use the profiles in the [http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl JASPAR Transcription Factor Binding Profile Database]. ([[media:T_Promoter_CDH2_AP2_2000updn_setup_logo.png|Screenshot Logo]], [[media:T_Promoter_CDH2_AP2_2000updn_scan.png|Screenshot Sequence 1]], [[media:T_Promoter_CDH2_AP2_2000updn_scan_fullseq.png|Screenshot Sequence 2]])
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Mark-Us||Released||Assesses the biochemical function for a given protein structure.
+
|width="150"|Sequence Alignment||Released||Run jobs on the NCBI BLAST servers directly within geWorkbench.  
 
|-
 
|-
 
|-
 
|-
−
|width="150"|MatrixReduce||Released||Transcription Factor binding motifs.
+
|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.
 
|-
 
|-
 
|-
 
|-
−
|width="150"|MEDUSA||Development||The 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 at MSKCC).
+
|width="150"|Sequence Retriever||Released||Retrieve sequences for annotated markers from Santa Cruz (Nucleotides) and EBI (Proteins). ([[media:T_SequenceRetriever_AfterRetrieval.png|Screenshot]])
 
|-
 
|-
 
|-
 
|-
−
|width="150"|MRA||Released||Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis.
+
|}
 +
 
 +
 
 +
==Visualization==
 +
 
 +
{|class = "wikitable" style="border: 1px solid lightGray"
 +
!Plugin||Status||Description
 
|-
 
|-
 
|-
 
|-
−
|width="150"|PCA||Released||Principal Component Analysis (from GenePattern).
+
|width="150"|Analysis Panel||Released||Framework to support numerous, individually loadable analysis methods.  
 
|-
 
|-
 
|-
 
|-
−
|width="150"|Pudge||Released ||Computational protein structure prediction using sequence homology. It integrates tools used at different stages of the structural prediction process.
+
|width="150"|ANOVA Tabular Viewer||Released||Displays the results of ANOVA analysis of gene expression  data in tabular format. ([[media:T_ANOVA_Tabular_Viewer.png|Screenshot]])
 +
|-
 +
|-
 +
|width="150"|CEL Image Viewer||Released||Visualization of data in Affymetrix CEL files. ([[media:T_CEL_viewer.png|Screenshot]])
 +
|-
 
|-
 
|-
 +
|width="150"|Color Mosaic||Released||Heat maps for microarray expression data, organized by phenotypic or gene groupings. ([[media:GeWB_Color_Mosaic_Viewer.png|Screenshot]])
 +
|-
 +
|-
 +
|width="150"|Dendrogram||Released||Tree-structured diagrams reflecting the results of hierarchical clustering analysis. ([[media:T_HC_Dendrogram_display.png|Screenshot]])
 
|-
 
|-
−
|width="150"|SkyBase||Development||Database of protein structure models produced by SkyLine based on structures solved by the NESG structural genomics consortium.
+
|-
 +
|width="150"|Evidence Integration Viewer||Development||Displays the results of the Evidence Integration analysis.
 
|-
 
|-
 
|-
 
|-
−
|width="150"|SkyLine||Development||Automated high-throughput pipeline for reverse homology-based comparative protein structure modeling based on the input template structure.
+
|width="150"|Expression Profiles||Released||Line graph of genes expression profiles across several arrays/ hybridizations. ([[media:GeWB_Expression_Profile_2markers.png|Screenshot]])
 
|-
 
|-
 
|-
 
|-
−
|width="150"|SOM||Released||Clustering of markers using Self Organizing Maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.
+
|width="150"|Expression Value Distribution||Released||Distribution plot of marker expression values across one or more microarrays. ([[media:T_EVD.png|Screenshot]])
 
|-
 
|-
 
|-
 
|-
−
|width="150"|SVM||Released||Support Vector Machine is a supervised classification method that computes a maximal separating hyperplane between the expression vectors of different classes or phenotypes (from GenePattern).
+
|width="150"|GeneWays||Released||An essential component needed to display elements in Cytoscape and ARACNe.
 +
|-
 +
|-
 +
|width="150"|GO Terms Viewer||Released||Displays the results of Gene Ontology Enrichment Analysis. ([[media:T_GO_Terms_TableBrowser_Gene_Detail.png|Screenshot]])
 +
|-
 +
|-
 +
|width="150"|Image Viewer||Released||Visualization of screenshots saved within geWorkbench (e.g. dendrograms).
 +
|-
 +
|-
 +
|width="150"|Jmol||Released|| Visualization of 3D protein structures from PDB files. ([[media:T_JMOL_Viewer.png|Screenshot]])
 +
|-
 +
|-
 +
|width="150"|Mark-Us Browser||Released|| Displays the results of a Mark-Us analysis. ([[media:T_MarkUs_Web_result.png|Screenshot]])
 +
|-
 
|-
 
|-
 +
|width="150"|MatrixReduce||Released||Visualization of MatrixReduce calculations using logo, chromosomal and tabular displays.
 +
|-
 
|-
 
|-
−
|width="150"|T-Test||Released||Identification of markers with statistically significant differential expression between sets of microarrays. ([[media:Volcanoplot.png|screenshot]]).
+
|width="150"|MEDUSA Viewer||Development||Displays the results of a MEDUSA analysis.
 +
|-
 
|-
 
|-
 +
|width="150"|Microarray Viewer||Released||Color-gradient representation of gene expression values. ([[media:GeWB_Microarray_Viewer.png|Screenshot]])
 +
|-
 
|-
 
|-
−
|width="150"|Weighted Voting||Released||Weighted Voting Analysis (from GenePattern).
+
|width="150"|MINDy Viewer||Released||The results of a MINDy calculation are presented in several different tabular displays and a heat map.
 +
|-
 
|-
 
|-
 +
|width="150"|MRA Viewer||Released||Displays the results of the MRA in tablular and graphical form. ([[media:MRA_viewer_full.png|Screenshot]])
 +
|-
 
|-
 
|-
−
|}
+
|width="150"|NetBoost Viewer||Development||Displays a Boosting Iteration Graph, Confusion Matrix and Score Table from NetBoost Analysis.
 +
|-
  
−
 
−
== Sequence Analysis & Visualization ==
 
−
 
−
{|style="border: 1px solid lightGray"
 
−
!Plugin||Status||Description
 
 
|-
 
|-
 +
|width="150"|Normalization Panel||Released||Framework to support numerous, individually loadable normalization components.
 
|-
 
|-
−
|width="150"|Alignment Results||Released||It parses and displays the results of sequence similarity searches which were run on the NCBI BLAST service.
 
 
|-
 
|-
 +
|width="150"|PCA Viewer||Released||Displays PCA results.
 
|-
 
|-
−
|width="150"|Pattern  Discovery||Released|| Discovery of sequence motifs in sets of DNA and protein sequences.
 
 
|-
 
|-
 +
|width="150"|Pudge Browser||Released||Visualization of Pudge results. ([[media:T_Pudge_Parameters.png|Screenshot Parameters]], [[media:T_Pudge_Alignment_example.png|Screenshot Result]])
 +
|-
 
|-
 
|-
−
|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]]).
+
|width="150"|Scatter Plot||Released||Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values. ([[media:GeWB_Scatter_Plot_array_vs_array.png|Screenshot Array]], [[media:GeWB_Scatter_Plot_marker_vs_marker.png|Screenshot Marker]])
 +
|-
 
|-
 
|-
 +
|width="150"|SkyBase Viewer||Released||Displays the results from the SkyBase search.
 +
|-
 
|-
 
|-
−
|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.]
+
|width="150"|SkyLine Output All||Released||Displays all models from the Skyline modeling.
 +
|-
 
|-
 
|-
 +
|width="150"|SkyLine Output Each||Released||Displays each model from the Skyline modeling.
 +
|-
 
|-
 
|-
−
|width="150"|Sequence Alignment||Released||Run jobs on the NCBI BLAST servers directly within geWorkbench.  
+
|width="150"|SkyLine Contour||Development||A 2D dominance-based visualization of query results.
 +
|-
 
|-
 
|-
 +
|width="150"|SOM Clusters Viewer||Released||Visualization of gene clusters produced by the self-organizing maps analysis. ([[media:T_SOM_result.png|Screenshot]])
 
|-
 
|-
−
|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.
 
 
|-
 
|-
 +
|width="150"|SVM Viewer||Released||Visualizes results obtained from classifying samples based on SVMs generated using the Gene Pattern v3 SVM service.
 +
|-
 
|-
 
|-
−
|width="150"|Sequence Retriever||Released||Retrieve sequences for annotated markers from Santa Cruz (nucleotide sequences) and EBI (proteins sequences).
+
|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:GeWB_Tabular_Microarray_Viewer.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]]).
+
|width="150"| Volcano Plot||Released|| Visualize fold-change vs significance (P-value) for t-test results. ([[media:T_t-test_volcano_BCELL_webm_qldm.png|Screenshot]])
−
|-
+
|-
 
|-
 
|-
 
|}
 
|}

Latest revision as of 10:17, 16 July 2013

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:


Status Comment
(a) Released This plugin is part of the latest geWorkbench version.
(b) Development This plugin is currently actively being developed.



Analysis

Plugin Status Description
ANOVA Released Analysis of Variance - detection of significant differences in expression between more than two groups. (Screenshot)
Evidence Integration Development A sequence and structure-based approach for functional annotation and protein-protein interaction analysis.
GSEA Released The Gene Set Enrichment Analysis determines whether an a priori defined set of genes shows statistically significant differences between two phenotypes.
Hierarchical Clustering Released Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin. (Screenshot)
KNN Released k-Nearest Neighbors analysis (a GenePattern component).
MatrixReduce Released Transcription Factor binding motifs. (Screenshot)
MEDUSA Development The 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).
MRA Released Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis. (Screenshot)
PCA Released Principal Component Analysis (a GenePattern component).
SOM Released Clustering of markers using Self Organizing Maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin. (Screenshot)
SVM 3.0 Released The 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-Test Released Identification of markers with statistically significant differential expression between sets of microarrays. (Screenshot Plot, Screenshot Mosaic)
Weighted Voting Released Weighted Voting Analysis (a GenePattern component).


Annotation

Plugin Status Description
caScript Development An Editor.
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 Enrichment 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 (caBIO Pathways/Cancer Gene Index); it includes visualization of BioCarta pathway diagrams. (Screenshot Table, Screenshot BioCarta, Screenshot CGI)


Data Filtering

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


Data Management

Plugin Status Description
Arrays/Phenotypes Released Definition of data views consisting of microarray subgroups. The views control the amount of data displayed. (Screenshot)
caArray Released Search and download of gene expression data from instances of caArray (NCI microarray database product). (Screenshot)
Markers Released Definition of data views consisting of marker subgroups. The views control the amount of data displayed. (Screenshot)
Project Folders Released Manages projects and workspaces of the user. (Screenshot)


File Import

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


Menu Tools

Plugin Status Description
CCM Released The Component Configuration Manager allows users to manage plugins dynamically at any given time in the application environment. (Screenshot)
genSpace Released It logs information about the analysis tools used in geWorkbench in order to enable collaboration support for the geWorkbench users.
Online Help Released geWorkbench Online Help uses the Java help 2.0 system to provide real-time help on component questions.
Preferences Released Allows users to predefine a few basic visual settings and choose a Text Editor.
Version Information Released Provides basic information about the currently installed user version of geWorkbench.
Welcome Screen Released Introduction to geWorkbench during the initial opening of the application.


Network Generation

Plugin Status Description
ARACNe Released The 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 GEMS Development Interface to the NCI Cancer Genetic Markers of Susceptibility project.
CNKB Released The 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)
Cytoscape Released Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 1.0. (Screenshot)
MINDy Released The Modulator Inference by Network Dynamics algorithm extends ARACNe to include detecting the influence of modulators of transcription factor activity.
NetBoost Development NetBoost is a network characterization algorithm.


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 Applies a log2 transformation to all measurements in a 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 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.


Protein Structure Analysis

Plugin Status Description
MarkUs Released Assesses the biochemical function for a given protein structure. (Screenshot)
Pudge Released Computational protein structure prediction using sequence homology. It integrates tools used at different stages of the structural prediction process. (Screenshot Parameters, Screenshot Result)
SkyBase Released Database of protein structure models produced by SkyLine based on structures solved by the NESG structural genomics consortium.
SkyLine Released Automated high-throughput pipeline for reverse homology-based comparative protein structure modeling based on the input template structure.


Sequence Analysis & Visualization

Plugin Status Description
Alignment Results Released It parses and displays the results of sequence similarity searches which were run on the NCBI BLAST service. (Screenshot)
Pattern Discovery Released 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 Analysis Released Identification 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 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 (Nucleotides) and EBI (Proteins). (Screenshot)


Visualization

Plugin Status Description
Analysis Panel Released Framework to support numerous, individually loadable analysis methods.
ANOVA Tabular Viewer Released Displays the results of ANOVA analysis of gene expression data in tabular format. (Screenshot)
CEL Image Viewer Released Visualization of data in Affymetrix CEL files. (Screenshot)
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)
Evidence Integration Viewer Development Displays the results of the Evidence Integration analysis.
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. (Screenshot)
GeneWays Released An essential component needed to display elements in Cytoscape and ARACNe.
GO Terms Viewer Released Displays the results of Gene Ontology Enrichment Analysis. (Screenshot)
Image Viewer Released Visualization of screenshots saved within geWorkbench (e.g. dendrograms).
Jmol Released Visualization of 3D protein structures from PDB files. (Screenshot)
Mark-Us Browser Released Displays the results of a Mark-Us analysis. (Screenshot)
MatrixReduce Released Visualization of MatrixReduce calculations using logo, chromosomal and tabular displays.
MEDUSA Viewer Development Displays the results of a MEDUSA analysis.
Microarray Viewer Released Color-gradient representation of gene expression values. (Screenshot)
MINDy Viewer Released The results of a MINDy calculation are presented in several different tabular displays and a heat map.
MRA Viewer Released Displays the results of the MRA in tablular and graphical form. (Screenshot)
NetBoost Viewer Development Displays a Boosting Iteration Graph, Confusion Matrix and Score Table from NetBoost Analysis.
Normalization Panel Released Framework to support numerous, individually loadable normalization components.
PCA Viewer Released Displays PCA results.
Pudge Browser Released Visualization of Pudge results. (Screenshot Parameters, Screenshot Result)
Scatter Plot Released Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values. (Screenshot Array, Screenshot Marker)
SkyBase Viewer Released Displays the results from the SkyBase search.
SkyLine Output All Released Displays all models from the Skyline modeling.
SkyLine Output Each Released Displays each model from the Skyline modeling.
SkyLine Contour Development A 2D dominance-based visualization of query results.
SOM Clusters Viewer Released Visualization of gene clusters produced by the self-organizing maps analysis. (Screenshot)
SVM Viewer Released Visualizes results obtained from classifying samples based on SVMs generated using the Gene Pattern v3 SVM service.
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. (Screenshot)
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