Difference between revisions of "Plugins"
| Line 31: | Line 31: | ||
|- | |- | ||
|- | |- | ||
| − | |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 | + | |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. | + | |width="150"|MRA||Released||The Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis. |
|- | |- | ||
|- | |- | ||
| Line 52: | Line 52: | ||
|- | |- | ||
|- | |- | ||
| − | |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"|SVM||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 (from GenePattern). |
|- | |- | ||
|- | |- | ||
| Line 70: | Line 70: | ||
|- | |- | ||
|- | |- | ||
| − | |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 | + | |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. |
|- | |- | ||
|- | |- | ||
| Line 94: | Line 94: | ||
|- | |- | ||
|- | |- | ||
| − | |width="150"|Marker Component ||Released||Definition of data views consisting of marker subgroups. The views control the amount of data displayed. | + | |width="150"|Marker Component||Released||Definition of data views consisting of marker subgroups. The views control the amount of data displayed. |
|- | |- | ||
|- | |- | ||
| − | |width="150"|Phenotype/Array Component ||Released||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed. | + | |width="150"|Phenotype/Array Component||Released||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed. |
|- | |- | ||
|- | |- | ||
| − | |width="150"|Project Component ||Released||Manages projects and workspaces of the user. | + | |width="150"|Project Component||Released||Manages projects and workspaces of the user. |
|- | |- | ||
|- | |- | ||
| Line 112: | Line 112: | ||
|- | |- | ||
|- | |- | ||
| − | |width="150"|Affy Detection Call||Released|| | + | |width="150"|Affy Detection Call||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"|Deviation Filter||Released||Filtering of markers with low dynamic range. |
|- | |- | ||
|- | |- | ||
| − | |width="150"|Expression Threshold||Released|| Elimination of measurements that fall outside a range of explression values. | + | |width="150"|Expression Threshold||Released||Elimination of measurements that fall outside a range of explression values. |
|- | |- | ||
|- | |- | ||
| − | |width="150"|2-channel Threshold||Released|| | + | |width="150"|2-channel Threshold||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|| | + | |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. | + | |width="150"|Missing Value Filter||Released||Discards all markers that have missing measurements in more than a user specified number N of microarrays. |
|- | |- | ||
|- | |- | ||
| Line 133: | Line 133: | ||
| − | ==Network Generation | + | ==Network Generation and Networking== |
{|style="border: 1px solid lightGray" | {|style="border: 1px solid lightGray" | ||
Revision as of 11:11, 12 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.
Contents
Analysis
| Plugin | Status | Description |
|---|---|---|
| ANOVA | Released | Analysis of Variance - detection of significant differences in expression between more than two groups. |
| Evidence Integration | Development | A sequence and structure-based approach for functional annotation and protein-protein interaction analysis. |
| Hierarchical Clustering | Released | Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin. |
| KNN | Released | k-Nearest Neighbors analysis (from GenePattern). |
| Mark-Us | Released | Assesses the biochemical function for a given protein structure. |
| MatrixReduce | Released | Transcription Factor binding motifs. |
| 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 | The Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis. |
| PCA | Released | Principal Component Analysis (from GenePattern). |
| Pudge | Released | 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 | Released | Clustering of markers using Self Organizing Maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin. |
| SVM | 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 (from GenePattern). |
| T-Test | Released | Identification of markers with statistically significant differential expression between sets of microarrays. (screenshot). |
| Weighted Voting | Released | Weighted Voting Analysis (from GenePattern). |
Annotation
| Plugin | Status | Description |
|---|---|---|
| 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. |
| 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 | 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. Includes visualization of BioCarta pathway diagrams (screenshot). |
Data Management
| Plugin | Status | Description |
|---|---|---|
| Marker Component | Released | Definition of data views consisting of marker subgroups. The views control the amount of data displayed. |
| Phenotype/Array Component | Released | Definition of data views consisting of microarray subgroups. The views control the amount of data displayed. |
| Project Component | Released | Manages projects and workspaces of the user. |
Filtering
| Plugin | Status | Description |
|---|---|---|
| Affy Detection Call | 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 | Released | Elimination of measurements that fall outside a range of explression values. |
| 2-channel Threshold | 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. |
Network Generation and Networking
| 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). |
| caArray | Released | 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. |
| 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. |
| Cytoscape | Released | Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 1.0(screenshot). |
| 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?". |
| 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 | The log2 transformation is applied to all measurements in a microarray, if all values in all microarrays are positive. |
| 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. |
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. |
| Pattern Discovery | Released | Discovery of sequence motifs in sets of DNA and protein sequences. |
| Position Histogram | Released | Visualization of results from the Pattern Discovery plugin. Motif/pattern support is plotted against relative sequence position of the motif match (screenshot). |
| Promoter Analysis | Released | Identification of putative transcription factor binding sites in DNA sequences (screenshot). The analysis use the profiles in the JASPAR Transcription Factor Binding Profile Database. |
| 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 (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 | 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. |
| CELImageViewer | Released | Visualization of data in Affymetrix CEL files. |
| 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. |
| GO Terms Viewer | Released | Displays the results of Gene Ontology Enrichment Analysis. |
| Image Viewer | Released | Visualization of screenshots saved within geWorkbench (e.g. dendrograms). |
| Jmol | Released | Visualization of 3D protein structures from PDB files. |
| Mark-Us Browser | Released | Displays the results of a MarkUs analysis. |
| 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. |
| 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. |
| Scatter Plot | Released | 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 | 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. |
