Plugins - Revision history

Floratos at 15:17, 16 July 2013

2013-07-16T15:17:27Z

Ut2102 at 15:34, 29 May 2013

2013-05-29T15:34:53Z

Smith at 21:06, 24 May 2011

2011-05-24T21:06:55Z

Smith at 21:50, 11 June 2010

2010-06-11T21:50:33Z

Smith at 21:50, 11 June 2010

2010-06-11T21:50:03Z

Zji at 21:46, 10 June 2010

2010-06-10T21:46:44Z

Zji at 21:43, 10 June 2010

2010-06-10T21:43:44Z

Smith at 19:48, 9 June 2010

2010-06-09T19:48:33Z

Smith at 19:47, 9 June 2010

2010-06-09T19:47:44Z

Smith at 19:46, 9 June 2010

2010-06-09T19:46:37Z

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 ==Analysis==
-{|style="border: 1px solid lightGray"
+{|class = "wikitable" style="border: 1px solid lightGray"
 !Plugin||Status||Description
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 ==Annotation==
-{|style="border: 1px solid lightGray"
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 ==Data Filtering==
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+{|class = "wikitable" style="border: 1px solid lightGray"
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 ==Data Management==
-{|style="border: 1px solid lightGray"
+{|class = "wikitable" style="border: 1px solid lightGray"
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 ==File Import==
-{|style="border: 1px solid lightGray"
+{|class = "wikitable" style="border: 1px solid lightGray"
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 ==Menu Tools==
-{|style="border: 1px solid lightGray"
+{|class = "wikitable" style="border: 1px solid lightGray"
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 ==Network Generation==
-{|style="border: 1px solid lightGray"
+{|class = "wikitable" style="border: 1px solid lightGray"
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 ==Normalization==
-{|style="border: 1px solid lightGray"
+{|class = "wikitable" style="border: 1px solid lightGray"
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 == Protein Structure Analysis ==
-{|style="border: 1px solid lightGray"
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 == Sequence Analysis & Visualization ==
-{|style="border: 1px solid lightGray"
+{|class = "wikitable" style="border: 1px solid lightGray"
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 ==Visualization==
-{|style="border: 1px solid lightGray"
+{|class = "wikitable" style="border: 1px solid lightGray"
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 |width="150"|KNN||Released||k-Nearest Neighbors analysis (a GenePattern component).
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 |width="150"|PCA||Released||Principal Component Analysis (a GenePattern component).
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 |width="150"|Threshold Normalizer||Released||Adjustment of values that fall outside a user-specified threshold.
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-|width="150"|GSEA||Development||The Gene Set Enrichment Analysis determines whether an a priori defined set of genes shows statistically significant differences between two phenotypes.
+|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.
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-|width="150"|Mark-Us||Released||Assesses the biochemical function for a given protein structure. ([[media:T_MarkUs_Web_result.png|Screenshot]])
+|width="150"|MarkUs||Released||Assesses the biochemical function for a given protein structure. ([[media:T_MarkUs_Web_result.png|Screenshot]])
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-|width="150"|MRA||Released||The Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis. ([[media:MRA_viewer_full.png|Screenshot]])
+|width="150"|MRA||Released||Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis. ([[media:MRA_viewer_full.png|Screenshot]])
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@@ Line 191: / Line 191: @@
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-|width="150"|CCM||Released||The Component Configuration Manager allows users to manage plugins dynamically at any given time in the application environment. ([[Image:CCM_Main.png|Screenshot]])
+|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]])
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-|width="150"|CCM||Released||The Component Configuration Manager allows users to manage plugins dynamically at any given time in the application environment. ([[media:T_Component_Configuration_Manager.png|Screenshot]])
+|width="150"|CCM||Released||The Component Configuration Manager allows users to manage plugins dynamically at any given time in the application environment. ([[Image:CCM_Main.png|Screenshot]])
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-|width="150"|SkyBase Viewer||Development||Displays the results from the SkyBase search.
+|width="150"|SkyBase Viewer||Released||Displays the results from the SkyBase search.
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-|width="150"|SkyLine Output All||Development||Displays all models from the Skyline modeling.
+|width="150"|SkyLine Output All||Released||Displays all models from the Skyline modeling.
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-|width="150"|SkyLine Output Each||Development||Displays each model from the Skyline modeling.
+|width="150"|SkyLine Output Each||Released||Displays each model from the Skyline modeling.
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-|width="150"|SkyBase||Development||Database of protein structure models produced by SkyLine based on structures solved by the NESG structural genomics consortium.
+|width="150"|SkyBase||Released||Database of protein structure models produced by SkyLine based on structures solved by the NESG structural genomics consortium.
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-|width="150"|SkyLine||Development||Automated high-throughput pipeline for reverse homology-based comparative protein structure modeling based on the input template structure.
+|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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 |width="150"|NetBoost||Development||NetBoost is a network characterization algorithm.
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 |width="120"|(b) Development||This plugin is currently actively being developed.
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@@ Line 55: / Line 55: @@
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 |width="150"|MRA||Released||The Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis. ([[media:MRA_viewer_full.png|Screenshot]])
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 |width="150"|SkyLine||Development||Automated high-throughput pipeline for reverse homology-based comparative protein structure modeling based on the input template structure.
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 |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]])
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 |width="150"|Expression Threshold Filter||Released||Elimination of measurements that fall outside a range of explression values.
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 |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]])
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 |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]])
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 |width="150"|Sequence Retriever||Released||Retrieve sequences for annotated markers from Santa Cruz (Nucleotides) and EBI (Proteins). ([[media:T_SequenceRetriever_AfterRetrieval.png|Screenshot]])
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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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 |width="150"|Normalization Panel||Released||Framework to support numerous, individually loadable normalization components.