Difference between revisions of "Plugins"
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|width="150"|Marker Component||Release||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.
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|width="150"|Marker Component||Release||Definition of data views consisting of marker subgroups. The views control the amount of data displayed. ([[media:Select_marker_sets.png|Screenshot]])
 
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|width="150"|Phenotype/Array Component||Release||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.
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|width="150"|Phenotype/Array Component||Release||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]])
 
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|width="150"|Project Component||Release||Manages projects and workspaces of the user.
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|width="150"|Project Component||Release||Manages projects and workspaces of the user. ([[media:T_ANOVA_Saved_Color_Mosaic_View.png|Screenshot]])
 
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Revision as of 16:37, 23 February 2010

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

The Status of the pluggable components below is defined as:


Status Comment
(a) Release This plugin is part of the latest geWorkbench version.
(b) Development This plugin is currently actively being developed.
(c) Suspension This plugin is currently not actively being developed.
(d) Discontinued This plugin is not part of geWorkbench anymore.



Analysis

Plugin Status Description
ANOVA Release 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.
Hierarchical Clustering Release Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin. (Screenshot)
KNN Release k-Nearest Neighbors analysis (a GenePattern component).
Mark-Us Release Assesses the biochemical function for a given protein structure. (Screenshot)
MatrixReduce Release 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 Release The Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis. (Screenshot)
PCA Release Principal Component Analysis (a GenePattern component).
Pudge Release Computational protein structure prediction using sequence homology. It integrates tools used at different stages of the structural prediction process.
SkyBase Development Database of protein structure models produced by SkyLine based on structures solved by the NESG structural genomics consortium.
SkyLine Development Automated high-throughput pipeline for reverse homology-based comparative protein structure modeling based on the input template structure.
SOM Release Clustering of markers using Self Organizing Maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin. (Screenshot)
SVM 3.0 Release 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 Release Identification of markers with statistically significant differential expression between sets of microarrays. (Screenshot Plot, Screenshot Mosaic)
Weighted Voting Release Weighted Voting Analysis (a GenePattern component).


Annotation

Plugin Status Description
Dataset Annotation Release Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online notebook.
Dataset History Release Log of data transformations induced by data-modifying operations.
Experiment Information Release 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 Release Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations. (Screenshot)
Marker Annotations Release 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 Release Filtering of measurements based on the value of their "detection call" attribute (Affymetrix data only) .
Deviation Filter Release Filtering of markers with low dynamic range.
Expression Threshold Release Elimination of measurements that fall outside a range of explression values.
2-channel Threshold Release Same as "Expression Threshold" filter but different threshold ranges can be specified for each channel (GenePix data only).
Genepix Flag Filter Release Filtering of measurements based on the value of their "Flags" attribute (GenePix data only).
Missing Value Filter Release Discards all markers that have missing measurements in more than a user specified number N of microarrays.


Data Management

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


File Import

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


Menu Tools

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


Network Generation

Plugin Status Description
ARACNe Release 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).
caArray Release Search and download of gene expression data from instances of caArray (NCI microarray database product).
Cancer GEMS Development Interface to the NCI Cancer Genetic Markers of Susceptibility project.
CNKB Release 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.
Cytoscape Release Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 1.0(screenshot).
MINDy Release 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 Release Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.
Housekeeping Normalizer Release Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.
Log2 Normalizer Release Applies a log2 transformation to all measurements in a microarray.
Marker-Based Centering Release Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.
Mean-Variance Normalizer Release 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 Release Replacement of missing values with consensus values.
Quantile Normalizer Release Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.
Threshold Normalizer Release Adjustment of values that fall outside a user-specified threshold.


Sequence Analysis & Visualization

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


Visualization

Plugin Status Description
Analysis Panel Release Framework to support numerous, individually loadable analysis methods.
ANOVA Tabular Viewer Release Displays the results of ANOVA analysis of gene expression data in tabular format.
CEL Image Viewer Release Visualization of data in Affymetrix CEL files.
Color Mosaic Release Heat maps for microarray expression data, organized by phenotypic or gene groupings (screenshot).
Dendrogram Release 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 Release Line graph of genes expression profiles across several arrays/ hybridizations (screenshot).
Expression Value Distribution Release Distribution plot of marker expression values across one or more microarrays.
GeneWays Release An essential component needed to display elements in Cytoscape and ARACNe.
GO Terms Viewer Release Displays the results of Gene Ontology Enrichment Analysis.
Image Viewer Release Visualization of screenshots saved within geWorkbench (e.g. dendrograms).
Jmol Release Visualization of 3D protein structures from PDB files.
Mark-Us Browser Release Displays the results of a Mark-Us analysis.
MatrixReduce Release Visualization of MatrixReduce calculations using logo, chromosomal and tabular displays.
MEDUSA Viewer Development Displays the results of a MEDUSA analysis.
Microarray Viewer Release Color-gradient representation of gene expression values (screenshot).
MINDy Viewer Release The results of a MINDy calculation are presented in several different tabular displays and a heat map.
MRA Viewer Release Displays the results of the MRA in tablular and graphical form.
NetBoost Viewer Development Displays a Boosting Iteration Graph, Confusion Matrix and Score Table from NetBoost Analysis.
Normalization Panel Release Framework to support numerous, individually loadable normalization components.
PCA Viewer Release Displays PCA results.
Pudge Browser Release Visualization of Pudge results.
Scatter Plot Release Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values (screenshot).
SkyBase Viewer Development Displays the results from the SkyBase search.
SkyLine Output All Development Displays all models from the Skyline modeling.
SkyLine Output Each Development Displays each model from the Skyline modeling.
SOM Clusters Viewer Release Visualization of gene clusters produced by the self-organizing maps analysis (screenshot).
SVM Viewer Release Visualizes results obtained from classifying samples based on SVMs generated using the Gene Pattern v3 SVM service.
Tabular Microarray Viewer Release Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray (screenshot).
Volcano Plot Release Visualize fold-change vs significance (P-value) for t-test results.
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