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Software

For microarray data analysis, we have several commercial software packages in-house. They can meet most investigators' data mining needs. In addition, there is an increasing number of open-source programs freely available for specific tasks.



Gene Network from PathwayAssist


Hierarchical Clustering

In-House Commercial Data-Mining Packages

- GeneSpring: a powerful visualization and analysis solution designed for use with genomic expression data. Capable of displaying and analyzing large datasets on typical desktop computers. Developed by Silicon Genetics, now acquired by Agilent. Supported by K-INBRE (Kansas IDeA Network of Biomedical Research Excellence) Program.

- GeneTraffic: a server-based system allowing users to import, visualize, analyze, interpret and store microarray data in a complete, secure data management environment. Developed by Iobion. Click here to log in.

- PathwayAssist: a pathway analysis software helping investigators to interpret experiment results in the context of pathways, gene regulation networks and protein interaction maps. Using curated and automatically created databases, PathwayAssist identifies relationships among genes, small molecules, cell objects and processes, builds networks and creates pathway diagrams good for publication. From Ariadne Genomics.

- Spotfire DecisionSite for Functional Genomics: providing an environment for investigators to analyze a variety of gene expression data, genomic data, proteomics data, pathway information, Gene Ontologies. From Spotfire.


BioConductor


GenMAPP

Open Source Software

The Facility also provides support for the following open source software:

- GenMAPP
- dChip
- RMAExpress
- Cytoscape

BioConductor is an open source and open development software project for the analysis and comprehension of genomic data. It provides a variety of data analysis tools for data mining purposes. The facility is in the process of adopting these tools for array data analysis.

A list of currently available open source programs is provided under "Favorite links" .