Microarray Data Analysis Solutions
commercial | free or open source
- 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
- 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.
- 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.