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.
  
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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:
  
  
−
==Microarray Visualization==
 
 
{|style="border: 1px solid lightGray"
 
{|style="border: 1px solid lightGray"
−
!Plugin||Description||Compatibility
+
!Status||Comment
 
|-
 
|-
 
|-
 
|-
−
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
+
|width="120"|(a) Released||This plugin is part of the latest geWorkbench version.
 
|-
 
|-
 +
|width="120"|(b) Development||This plugin is currently actively being developed.
 
|-
 
|-
 +
|-
 +
|}
 +
 +
 +
 +
__TOC__
 +
 +
 +
==Analysis==
  
−
|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
+
{|class = "wikitable" style="border: 1px solid lightGray"
 +
!Plugin||Status||Description
 +
|-
 +
|-
 +
|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"|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"|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]])
 
|-
 
|-
−
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
+
|-
 +
|width="150"|PCA||Released||Principal Component Analysis (a GenePattern component).
 
|-
 
|-
 
|-
 
|-
−
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
+
|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"|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"|Weighted Voting||Released||Weighted Voting Analysis (a GenePattern component).
 
|-
 
|-
 +
|-
 +
|}
 +
 +
 +
==Annotation==
  
−
|Microarray Panel||Color-gradient representation of measured gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
+
{|class = "wikitable" style="border: 1px solid lightGray"
−
|-
+
!Plugin||Status||Description
 +
|-
 +
|-
 +
|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"|Dataset History||Released||Log of data transformations induced by data-modifying operations.
 +
|-
 +
|-
 +
|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"|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"|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]])
 +
|-
 
|-
 
|-
 +
|}
 +
 +
 +
==Data Filtering==
  
−
|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
+
{|class = "wikitable" style="border: 1px solid lightGray"
−
|-
+
!Plugin||Status||Description
 +
|-
 +
|-
 +
|width="150"|Affy Detection Call Filter||Released||Filtering of measurements based on the value of their "detection call" attribute ''(Affymetrix data only)'' .
 +
|-
 +
|-
 +
|width="150"|Deviation Filter||Released||Filtering of markers with low dynamic range.
 +
|-
 +
|-
 +
|width="150"|Expression Threshold Filter||Released||Elimination of measurements that fall outside a range of explression values.
 +
|-
 +
|-
 +
|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"|Genepix Flag Filter||Released||Filtering of measurements based on the value of their "Flags" attribute ''(GenePix data only)''.
 +
|-
 
|-
 
|-
−
 
+
|width="150"|Missing Value Filter||Released||Discards all markers that have missing  measurements in more than a user specified number N of microarrays.
−
|SOM Clusters ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
 
−
|-
 
 
|-
 
|-
−
 
−
|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
 
 
|-
 
|-
 
|}
 
|}
 +
  
 
==Data Management==
 
==Data Management==
−
{|style="border: 1px solid lightGray"
+
 
−
!Plugin||Description||Compatibility
+
{|class = "wikitable" style="border: 1px solid lightGray"
 +
!Plugin||Status||Description
 
|-
 
|-
 
|-
 
|-
−
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control how much data is displayed by only using values for markers in the defined groups.||TBD
+
|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"|Markers||Released||Definition of data views consisting of marker subgroups. The views control the amount of data displayed. ([[media:Select_marker_sets.png|Screenshot]])
 
|-
 
|-
 
|-
 
|-
−
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control how much data is displayed by only using values for microarrays in the defined groups.||TBD
+
|width="150"|Project Folders||Released||Manages projects and workspaces of the user. ([[media:T_ANOVA_Saved_Color_Mosaic_View.png|Screenshot]])
 
|-
 
|-
 
|-
 
|-
 
|}
 
|}
  
−
==Normalizers==
+
 
−
{|style="border: 1px solid lightGray"
+
==File Import==
−
!Plugin||Description||Compatibility
+
 
 +
{|class = "wikitable" style="border: 1px solid lightGray"
 +
!Plugin||Status||Description
 +
|-
 +
|-
 +
|width="150"|Affymetrix CEL||Released||Loads Affymetrix probe CELl intensity files ("*.cel").
 +
|-
 
|-
 
|-
−
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
+
|width="150"|Affymetrix File Matrix||Released|| Loads Affymetrix EXPperiment files ("*.exp").
 
|-
 
|-
 
|-
 
|-
−
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
+
|width="150"|Affymetrix MAS5/GCOS||Released|| Loads output files from the GeneChip Operating Software formerly known as MAS5 Statistical algorithm (several different file extension).
 
|-
 
|-
 
|-
 
|-
−
|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"|FASTA Format||Released||Loads files that are in FASTA format ("*.fasta" and "*.txt").
−
||TBD
 
 
|-
 
|-
 
|-
 
|-
−
|Missing Value Calculation||Replacement of missing values with consensus values.
+
|width="150"|Genepix File Format||Released||Loads files in GenePix Result format ("*.gpr").
−
||TBD
 
 
|-
 
|-
 
|-
 
|-
−
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
+
|width="150"|PDB Structure Format||Released||Loads files in the Protein Data Base format ("*.pdb")
 
|-
 
|-
−
|Quantile || Expression measurements in each microarray are adjusted so that  expression value distribution is the same across all microarrays in an experiment.||TBD
 
 
|-
 
|-
 +
|width="150"|Tab-delimited (RMA Express Format)||Released||Loads tab-delimited files from the Robust Multichip Analysis ("*.txt")
 
|-
 
|-
−
|Housekeeping || Measurements are divided by the average expression value of a (user defined) set of housekeeping genes.||TBD
 
 
|-
 
|-
 +
|}
  
−
|}
 
  
−
==Annotation==
+
==Menu Tools==
  
−
{|style="border: 1px solid lightGray"
+
{|class = "wikitable" style="border: 1px solid lightGray"
−
!Plugin||Description||Compatibility
+
!Plugin||Status||Description
 +
|-
 +
|-
 +
|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]]) 
 
|-
 
|-
−
|Dataset History||Log of data transformations induced by data-modifying operations.||?
 
 
|-
 
|-
 +
|width="150"|genSpace||Released||It logs information about the analysis tools used in geWorkbench in order to enable collaboration support for the geWorkbench users.
 
|-
 
|-
−
|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".||?
 
 
|-
 
|-
 +
|width="150"|Online Help||Released||geWorkbench Online Help uses the Java help 2.0 system to provide real-time help on component questions.
 
|-
 
|-
−
|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||?
 
 
|-
 
|-
 +
|width="150"|Preferences||Released||Allows users to predefine a few basic visual settings and choose a Text Editor.
 
|-
 
|-
−
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
 
 
|-
 
|-
 +
|width="150"|Version Information||Released||Provides basic information about the currently installed user version of geWorkbench.
 
|-
 
|-
−
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
 
 
|-
 
|-
−
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
+
|width="150"|Welcome Screen||Released||Introduction to geWorkbench during the initial opening of the application.
 
|-
 
|-
 
|-
 
|-
 
|}
 
|}
 +
  
 
==Network Generation==
 
==Network Generation==
  
−
{|style="border: 1px solid lightGray"
+
{|class = "wikitable" style="border: 1px solid lightGray"
−
!Plugin||Description||Compatibility
+
!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:T_ARACNE_result1.png|Screenshot]])
 +
|-
 +
|-
 +
|width="150"|Cancer GEMS||Development||Interface to the NCI Cancer Genetic Markers of Susceptibility project.
 +
|-
 +
|-
 +
|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"|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]])
 
|-
 
|-
−
|ARACNE Reverse Engineering|| Analyzes a large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks.||?
 
 
|-
 
|-
 +
|width="150"|MINDy||Released||The Modulator Inference by Network Dynamics algorithm extends ARACNe to include detecting the influence of modulators of transcription factor activity.
 
|-
 
|-
 
|-
 
|-
−
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 2.0 (http://www.cytoscape.org/). ||?
+
|width="150"|NetBoost||Development||NetBoost is a network characterization algorithm.
 
|-
 
|-
 
|}
 
|}
  
−
==Analysis==
 
  
−
{|style="border: 1px solid lightGray"
+
==Normalization==
−
!Plugin||Description||Compatibility
+
 
 +
{|class = "wikitable" style="border: 1px solid lightGray"
 +
!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"|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"|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.
 
|-
 
|-
−
|Hierarchical Clustering||Hierarchical clustering groups markers into clusters on the basis of similarities in their expression profiles to form a hierarchical tree that can be viewed in the Dendrogram View window.||?
 
 
|-
 
|-
 +
|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.
 
|-
 
|-
−
|Self Organizing Map (SOM)|| An algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||?
 
 
|-
 
|-
 +
|width="150"|Threshold Normalizer||Released||Adjustment of values that fall outside a user-specified threshold.
 
|-
 
|-
−
|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform (http://www.tm4.org/mev.html).||?
 
 
|-
 
|-
 +
|}
 +
 +
 +
== Protein Structure Analysis ==
  
−
|}
+
{|class = "wikitable" style="border: 1px solid lightGray"
−
== Sequence Analysis==
+
!Plugin||Status||Description
−
{|style="border: 1px solid lightGray"
+
|-
−
!Plugin||Description||Compatibility
+
|-
 +
|width="150"|MarkUs||Released||Assesses the biochemical function for a given protein structure. ([[media:T_MarkUs_Web_result.png|Screenshot]])
 +
|-
 +
|-
 +
|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"|SkyBase||Released||Database of protein structure models produced by SkyLine based on structures solved by the NESG structural genomics consortium.
 +
|-
 
|-
 
|-
 +
|width="150"|SkyLine||Released||Automated high-throughput pipeline for reverse homology-based comparative protein structure modeling based on the input template structure.
 
|-
 
|-
−
|Synteny|| A utility for comparison of extended genomic regions.-||?
 
−
 
 
|-
 
|-
 
|}
 
|}
  
−
== Pattern Discovery==
+
 
−
{|style="border: 1px solid lightGray"
+
== Sequence Analysis & Visualization ==
−
!Plugin||Description||Compatibility
+
 
 +
{|class = "wikitable" style="border: 1px solid lightGray"
 +
!Plugin||Status||Description
 +
|-
 +
|-
 +
|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"|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"|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]])
 
|-
 
|-
−
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ).  The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?
 
−
 
 
|-
 
|-
 +
|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]])
 
|-
 
|-
−
 
−
|Sequence Alignment||--.||?
 
 
|-
 
|-
−
 
+
|width="150"|Sequence Alignment||Released||Run jobs on the NCBI BLAST servers directly within geWorkbench.
 
|-
 
|-
−
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?
 
−
 
 
|-
 
|-
 +
|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.
 
|-
 
|-
−
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
 
 
|-
 
|-
 +
|width="150"|Sequence Retriever||Released||Retrieve sequences for annotated markers from Santa Cruz (Nucleotides) and EBI (Proteins). ([[media:T_SequenceRetriever_AfterRetrieval.png|Screenshot]])
 
|-
 
|-
−
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
 
 
|-
 
|-
 
|}
 
|}
−
== Filters==
 
  
−
{|style="border: 1px solid lightGray"
+
 
−
!Plugin||Description||Compatibility
+
==Visualization==
 +
 
 +
{|class = "wikitable" style="border: 1px solid lightGray"
 +
!Plugin||Status||Description
 +
|-
 +
|-
 +
|width="150"|Analysis Panel||Released||Framework to support numerous, individually loadable analysis methods.
 +
|-
 +
|-
 +
|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"|Evidence Integration Viewer||Development||Displays the results of the Evidence Integration analysis.
 +
|-
 +
|-
 +
|width="150"|Expression Profiles||Released||Line graph of genes expression profiles across several arrays/ hybridizations. ([[media:GeWB_Expression_Profile_2markers.png|Screenshot]])
 +
|-
 +
|-
 +
|width="150"|Expression Value Distribution||Released||Distribution plot of marker expression values across one or more microarrays. ([[media:T_EVD.png|Screenshot]])
 +
|-
 
|-
 
|-
 +
|width="150"|GeneWays||Released||An essential component needed to display elements in Cytoscape and ARACNe.
 
|-
 
|-
−
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing.  ||TBD
 
 
|-
 
|-
 +
|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]])
 +
|-
 
|-
 
|-
−
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
+
|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.
 +
|-
 
|-
 
|-
−
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
+
|width="150"|MEDUSA Viewer||Development||Displays the results of a MEDUSA analysis.
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|-
 
|-
 
|-
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|width="150"|Microarray Viewer||Released||Color-gradient representation of gene expression values. ([[media:GeWB_Microarray_Viewer.png|Screenshot]])
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|-
−
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
+
|width="150"|MINDy Viewer||Released||The results of a MINDy calculation are presented in several different tabular displays and a heat map.
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|-
 
|-
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|width="150"|MRA Viewer||Released||Displays the results of the MRA in tablular and graphical form. ([[media:MRA_viewer_full.png|Screenshot]])
 +
|-
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|-
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|width="150"|NetBoost Viewer||Development||Displays a Boosting Iteration Graph, Confusion Matrix and Score Table from NetBoost Analysis.
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|-
  
 
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|-
−
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
+
|width="150"|Normalization Panel||Released||Framework to support numerous, individually loadable normalization components.
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|-
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|-
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|width="150"|PCA Viewer||Released||Displays PCA results.
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|-
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|-
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|width="150"|Pudge Browser||Released||Visualization of Pudge results. ([[media:T_Pudge_Parameters.png|Screenshot Parameters]], [[media:T_Pudge_Alignment_example.png|Screenshot Result]])
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|-
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|-
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|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]])
 +
|-
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|-
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|width="150"|SkyBase Viewer||Released||Displays the results from the SkyBase search.
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|-
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|width="150"|SkyLine Output All||Released||Displays all models from the Skyline modeling.
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|-
−
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
+
|width="150"|SkyLine Output Each||Released||Displays each model from the Skyline modeling.
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|-
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|width="150"|SkyLine Contour||Development||A 2D dominance-based visualization of query results.
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|width="150"|SOM Clusters Viewer||Released||Visualization of gene clusters produced by the self-organizing maps analysis. ([[media:T_SOM_result.png|Screenshot]])  
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|-
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|width="150"|SVM Viewer||Released||Visualizes results obtained from classifying samples based on SVMs generated using the Gene Pattern v3 SVM service.
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|-
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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:GeWB_Tabular_Microarray_Viewer.png|Screenshot]])
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|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]])
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|}
 
|}

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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