TM4 – TM4 is a microarray softare suite including four major applications and a mySQL database. Open source, originally developed at TIGR.
Cluster and Treeview – An integrated pair of programs for analyzing and visualizing the results of complex microarray experiments. Both written by Michael Eisen.
Bioconductor Array Workflow – Bioconductor includes extensive support for analysis of expression arrays, and well-developed support for exon, copy number, SNP, methylation, and other assays. Major workflows in Bioconductor include pre-processing, quality assessment, differential expression, clustering and classification, gene set enrichment analysis, and genetical genomics.
GEXC – GEXC (Gene Expression Commons) provides absolute common reference by global-scale meta analysis of publicly available microarray data.
Genevestigator – Genevestigator is an innovative online platform enabling researchers to globally explore public and proprietary expression data for research and clinical applications.