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Statistical Bioinformatics

Statistical Analysis Software for Microarray Data

Institutions or companies which produce data analysis software for cDNA microarray slides.

Note that I am no longer updating this list.

• BASE (BioArray Software Environment). Microarray database server with normalization and some analysis facilities. Lund University, Sweden.
• Bengtsson, Henrik. Develops aroma, an elegant R package for microarray normalization, diagnostics and data analysis using a custom object-orientated system.
• Bioconductor. An R-based development project for open-source genomic software. Includes a number of important packages. Coordinated by Robert Gentleman, Fred Hutchinson Cancer Center.
• BioSieve. Produce ExpressionSieve, a microarray data analysis, data mining and data visualization software package written in Java.
• Broad Institute of MIT and Harvard. Produce the GenePattern package for genomics and microarray analysis.
• Eisen Lab. Distribute ScanAlyze, Cluster and TreeView free for non-profit researchers.
• Biodiscovery. GeneSight.
• Genedata. Produce Expressionist software for large scale gene expression analysis.
• GeneSifter.Net. A web-based data analysis tool for Affymetrix microarrays created by VizX Labs, Seattle.
• Gerstein Lab (Yale University). ExpressYourself is an online platform for pre-preprocessing of microarray data.
• InforMax (Array Pro, Vector Xpression).
• Iobian Informatics. GeneTraffic is microarray database and data analysis software based on open software.
• Molecular Devices. Acuity for data warehousing, analysis and visualization.
• Molmine (J-Express). Java software.
• National Center for Genome Resources (GeneX).
• PAM: Prediction Analysis for Microarrays. Robert Tibshirani, Stanford University.
• Pevsner Lab, (Kennedy Kreiger Institute). SNOMAD (Standardization and NOrmalization of MicroArray Data).
• Partek. Produce Partek Pro software for statistical analysis and visualisation including gene expression.
• PermutMatrix. MS Windows software for clustering and seriation analysis of gene expression data. Gilles Caraux, LIRMM, France.
• Churchhill Lab (Jackson Laboratories). maanova for analysis of variance with microarray data.
• Rosetta Inpharmatics. No links to software on their www pages.
• Silicon Genetics. Genespring is a very popular program for general data analysis of microarray data.
• SilicoCyte. Integrated commercial analysis solution.
• Spotfire. DecisionSite software for functional analysis.
• Speed Group (University of California, Berkeley). R package sma (Statistical Microarray Analysis), Windows application RMAExpress and contributions to the Bioconductor project.
• TIGR. SpotFinder image analysis, MIDAS data management, MeV differential expression analysis.
• Probability of Expression (POE). An approach to the analysis of gene expression microarrays using three-component mixtures. Giovanni Parmigiani, Johns Hopkins.
• SuperArray.
• Townsend Lab, University of Connecticut. Produces BAGEL (Bayesian Analysis of Gene Expression Levels) for the statistical analysis of spotted microarray data, Pathway Processor to test for overrepresentation of differentially expressed genes within known pathways of S. cerevisiae or B. subtilis, and SeqPop for computing population genetics statistics on sequence data.
• University of Pittsburgh & UPMC Bioinformatics Web-Tools Collection. Includes expression analysis tool with www interface.
• Walter and Eliza Hall Institute of Medical Research. Produce R package limma (linear models and differential expression for microarray data) and associated user-interfaces limmaGUI and affylmGUI.
• Wong Lab (Harvard University). DNA-Chip Analyzer.
• Yang, Jean (University of Sydney). R packages marray, DEDS and stepNorm.