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Some network visualization/analysis tools have built-in graph analysis features such as: * Shortest path * Cluster analysis * Graph traverse * Graph Statistics: * Mean shortest path * Degree distribution * Average number of interaction partners * Clustering coefficient * Topological coefficient |
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Some of these are implemented as Cytoscape plugins, but there is no one simple plugin to provide all of these. The purpose of this project is creating a core plugin to provide all of these functionality. |
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Functions needs to be implementd: * (Please add functions we need to implement...) |
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=== Software with Graph Analysis Functionalities === * [http://vlado.fmf.uni-lj.si/pub/networks/pajek/ Pajek] * [http://jung.sourceforge.net/ JUNG] * [http://cneurocvs.rmki.kfki.hu/igraph/ igraph] * |
RFC Name : Consolicated Graph Analysis Plugin |
Editor(s): Keiichiro Ono |
Status: Open for Comments |
Proposal
This document is for consolidated graph analysis plugin development plan.
Biological Questions / Use Cases
Some network visualization/analysis tools have built-in graph analysis features such as:
- Shortest path
- Cluster analysis
- Graph traverse
- Graph Statistics:
- Mean shortest path
- Degree distribution
- Average number of interaction partners
- Clustering coefficient
- Topological coefficient
Some of these are implemented as Cytoscape plugins, but there is no one simple plugin to provide all of these. The purpose of this project is creating a core plugin to provide all of these functionality.
General Notes
Requirements
Deferred Items
Open Issues
Functions needs to be implementd:
- (Please add functions we need to implement...)
Backward Compatibility
Expected growth and plan for growth
References
Software with Graph Analysis Functionalities
[http://jung.sourceforge.net/ JUNG]
Implementation Plan
Comments
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