Microarray Data Analysis Solutions

• BioMine (Gene Network Sciences), DNA microarray analysis package, with flexible data import, normalization, several clustering algorithms, and more.
• GeneSight™ (Biodiscovery), user-friendly data analysis and data mining tool specifically designed for microarray data
• GeneSifter.net, web-based microarray data analysis, integrating statistics, biology, and ontology information.
• GeneSpring™ (Silicon Genetics), analytical workbench that enables scientists to visualize, organize and manipulate gene expression data
• Insightful S+ArrayAnalyzer®, features rigorous statistical analysis, interactive graphical reporting, publication quality output, and extensible development environment.
• Koadarray software for automated analysis and quantification of microarray images.
• MATLAB Bioinformatics Toolbox, provides access to genomic and proteomic data, analysis, and visualizations for sequences and microarrays.
• Probe Profiler, reduces variability of Affymetrix GeneChip data by analyzing consistency in behavior of the probe pairs and their prediction efficiency.
• Rosetta Resolver® Gene Expression Analysis System, includes tools and features for high-powered analysis, visualization and storage of gene expression data.

• NIH Microarray Consortium, providing NIH funded neuroscience investigators with the opportunity to use gene expression profiling technology and SNP genotyping, through acquisition and dissemination of high quality array based data.
• Bioconductor, R-based open source bioinformatics software, primarily for DNA microarrays.
• caArray suite of tools from NCI, including caWorkbench and webCGH.
• Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data.
• FatiGO (Datamining with Gene Ontology) and other microarray tools.
• Free PubGene service, for analyzing gene expression data with literature network information.
• GenMAPP, software for visualizing gene expression data on maps representing biological pathways and groupings of genes.
• MAExplorer - MicroArray Explorer, (Java) exploratory environment for data mining across multiple microarrays.
• National Cancer Institute (NCI) Director's Challenge, toward a molecular classification of cancer. Provides analytic tools, datasets, and more.
• NIH Genomics and Bioinformatics group, offering microarray data and tools, gene ontology tools, and more.
• PAM, Prediction Analysis of Microarrays, and
  SAM: Significance Analysis of Microarrays,
  from Tibshirani's group (Stanford), available as Excel add-in or R-package.
• PermutMatrix, graphical software for clustering and seriation analysis, with several types of hierarchical cluster analysis and several methods to find an optimal reorganization of rows and columns.
• ProbeExplorer, an open access web-based bioinformatic application for showing associations between microarray oligonucleotide probes and transcripts in the genomic context.