There are few interesting packages from the [Spatial Data Mining and Visual Analytics Lab][1], especially:

 - [**EntroMap**][2]: Detecting Spatially Varying Multivariate Relationships
 - [**VIS-STAMP**][3]: A Visualization System for Space-Time and Multivariate Patterns
 - [**SOMVIS**][4]: Multivariate Mapping and Visualization


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[S4 research group][5] also has few useful [tools][6], especially:

 - [**GéoGrapheur**][7]: Exploratory Data Analysis Module
 - [**Map Comparison Kit**][8] 
 - [**Darcy 2.0**][9]


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[**CrimeStat**][10] is also worth having a look. Although focused on crime analysis, the functionality can be adapted to other purposes.


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[**SANET**][11] is an ArcGIS toolset for analysis based on networks.


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[**GeoSOM**][12] is a package for creating spatial Self-Organizing Maps.


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Although lacking any mapping capabilities [**SaTScan**][13] is an essential tool for exploration of spatial and spatio-temporal clusters. [**Fast Spatial Scan**][14] from [The Auton Lab][15] can cope with larger datasets.


  [1]: http://www.spatialdatamining.org/software
  [2]: http://www.spatialdatamining.org/entromap
  [3]: http://www.spatialdatamining.org/software/visstamp
  [4]: http://www.spatialdatamining.org/software/somvis
  [5]: http://www.spatial-modelling.info/
  [6]: http://www.spatial-modelling.info/-Spatial-analysis-tools-
  [7]: http://www.spatial-modelling.info/GeoGrapheur
  [8]: http://www.spatial-modelling.info/Map-Comparison-Kit
  [9]: http://www.spatial-modelling.info/Darcy-2-module-de-comparaison
  [10]: http://www.icpsr.umich.edu/CrimeStat/
  [11]: http://sanet.csis.u-tokyo.ac.jp/
  [12]: http://www.isegi.unl.pt/labnt/geosom/index.htm
  [13]: http://www.satscan.org/
  [14]: http://www.autonlab.org/autonweb/16629.html
  [15]: http://www.autonlab.org/autonweb/2.html