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| ## page was renamed from GSoC2010_SoftwareDownload | |
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| = Semantic Network Summary Plugin Download Page = | = WordCloud Plugin Download Page = |
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| The Semantic Network Summary is a Cytsocape plugin 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. | The WordCloud Plugin is a Cytoscape plugin 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. |
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| === Current Version === Updated 10/14/10 * [[attachment:WordCloudPlugin_v1.0RC1.zip]] === Previous Versions === Updated 9/12/2010 * [[attachment:WordCloudPlugin_v1.0beta.zip]] |
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* [[attachment:SemanticNetworkSummary_v0.5.zip]] |
* [[attachment:SemanticNetworkSummary_v0.5.zip]] (The name of the plugin was previously `SemanticNetworkSummary`) |
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| [[attachment:AlzheimerEM.cys]] | * 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]] |
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| * [[GSoC2010_UseExamples|Guided tutorial]] on the basic functioning of the Semantic Network Summary plugin. * [[GSoC2010_ParameterTutorial|Parameter tutorial]] on using all of the parameters available for the Semantic Network Summary plugin. |
== Tutorials == * [[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 Plugin is a Cytoscape plugin 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
Updated 10/14/10
Previous Versions
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
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