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= Semantic Network Summary Plugin Download Page = | ## page was renamed from GSoC2010_SoftwareDownload #acl All:read LaylaOesper:write,delete,revert = WordCloud Plugin Download Page = |
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The Semantic Network Summary Cytoscape Plugin allows you to visualize a selected set of nodes in a network as a word tag cloud. It will operate on any Cytoscape network. The tag cloud can be built based up the words in the node ID's or the words appearing in any node attribute that is comprised of Strings, or a List of Strings. The size of the words appearing in the word tag cloud is representative of the word's importance for the node selection as a function of both the number of times the word appears in the selected nodes and the entire network for the selected node attribute. There are also options for viewing a clustered version of the word tag cloud. | The WordCloud App is a Cytoscape App that generates a word tag cloud from a user-defined node selection, summarizing an attribute of choice. For instance, if selected nodes are proteins, and the string attribute "full protein name" is selected, every string will be broken down into words, which will be plotted on a panel with size proportional to their frequency. It is also possible to use the plugin to cluster words that appear together in the selected nodes. For instance, if node A has name attribute "Origin Recognition Complex 1" and node B has name attribute "Origin Recognition Complex 2", then the words "Origin", "Recognition" and "Complex" will be clustered together, following the order in which they appear. The plugin operates on any network and on any selected attributes, although it has been specifically designed for string attributes such as gene names or gene ontology annotations. |
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Coming soon! | === Current Version (3.0) === * Install directly from the [[http://apps.cytoscape.org/apps/wordcloud|Cytoscape App Store]] * App Jar file available on [[https://github.com/BaderLab/WordCloudPlugin/releases|GitHub]] === Previous Versions === Updated 1/6/11 * [[attachment:WordCloudPlugin_v1.0RC2.zip]] Updated 10/14/10 * [[attachment:WordCloudPlugin_v1.0RC1.zip]] Updated 9/12/2010 * [[attachment:WordCloudPlugin_v1.0beta.zip]] Updated 7/20/2010 * [[attachment:SemanticNetworkSummary_v0.5.zip]] (The name of the plugin was previously `SemanticNetworkSummary`) == Sample Data Download == * gene/protein interaction networks * DNA Replication yeast: [[attachment:ReplDNA_v04.cys]] * gene-set networks (see [[Software/EnrichmentMap/Description|Enrichment map]]) * Gene-sets enriched in Alzheimer: [[attachment:AlzheimerEM.cys]] == Tutorials == Step by step tutorials that include expected output for one of the sample data download Cytoscape sessions provided above. * [[Software/WordCloudPlugin/BasicTutorial|Guided Basic Tutorial]] on the basic functioning of the WordCloud plugin. * [[Software/WordCloudPlugin/ParameterTutorial|Advanced Parameter Tutorial]] on using all of the parameters available for the WordCloud plugin. |
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[[GSoC2010_UserManual|User Guide Link]] | * [[Software/WordCloudPlugin/UserManual|User Guide Link]] == For Software Developers == * [[http://chianti.ucsd.edu/svn/csplugins/trunk/soc/layla/WordCloudPlugin/|Source code]] * [[Software/WordCloudPlugin/HowToReleaseWordCloudPlugin|How to release a new version of the WordCloud Plugin]] |
WordCloud Plugin Download Page
Brief Description
The WordCloud App is a Cytoscape App that generates a word tag cloud from a user-defined node selection, summarizing an attribute of choice. For instance, if selected nodes are proteins, and the string attribute "full protein name" is selected, every string will be broken down into words, which will be plotted on a panel with size proportional to their frequency.
It is also possible to use the plugin to cluster words that appear together in the selected nodes. For instance, if node A has name attribute "Origin Recognition Complex 1" and node B has name attribute "Origin Recognition Complex 2", then the words "Origin", "Recognition" and "Complex" will be clustered together, following the order in which they appear. The plugin operates on any network and on any selected attributes, although it has been specifically designed for string attributes such as gene names or gene ontology annotations.
Plugin Download
Current Version (3.0)
Install directly from the Cytoscape App Store
App Jar file available on GitHub
Previous Versions
Updated 1/6/11
Updated 10/14/10
Updated 9/12/2010
Updated 7/20/2010
SemanticNetworkSummary_v0.5.zip (The name of the plugin was previously SemanticNetworkSummary)
Sample Data Download
- gene/protein interaction networks
DNA Replication yeast: ReplDNA_v04.cys
gene-set networks (see Enrichment map)
Gene-sets enriched in Alzheimer: AlzheimerEM.cys
Tutorials
Step by step tutorials that include expected output for one of the sample data download Cytoscape sessions provided above.
Guided Basic Tutorial on the basic functioning of the WordCloud plugin.
Advanced Parameter Tutorial on using all of the parameters available for the WordCloud plugin.
User Guide