From Genome Technology Core (GTC) wiki - Sequencing and Microarray
Jump to: navigation, search
MIT Software
Program Description Platform
GSEA Determines if a given set of genes shows differences between two biological states JAVA
GeneCluster Self-organizing maps JAVA, Windows NT
Connectivity Map Uses pattern-matching algorithms to enable discovery of functional connections between drugs, genes, and diseases Web
GeneCruiser Annotation tool for Affymetrix probes Web
Free Software from other sources
Program Description Provider Platform
Array Designer Tool assisting in primer design for microarray construction Premier Biosoft International JAVA
ArrayMiner Set of analysis tools using advanced algorithms to reveal the true structure of gene expression data Optimal Design, Sprl. Windows/MacOS
ArrayViewer Identification of statistically significant hybridization signals National Human Genome Research Institute JAVA
BAGEL Bayesian Analysis of Gene Expression Levels: a program for the statistical analysis of spotted microarray data. University of Connecticut MacOS, Windows, Linux
BAMarray Bayesian Analysis of Variance for Microarrays - detect differentially expressed genes from multigroup microarray data Case University Windows, Linux
BASE Microarray database and analysis platform Lund University Web
Cluster 3.0 An enhanced version of Mike Eisen's Cluster University of Tokyo, Japan UNIX, Linux, MacOS, Windows
DNA arrays analysis tools Hierarchical clustering, Self Organizing Maps and more Spanish National Cancer Center, Bioinformatics Unit Web
Expression Profiler Analysis & clustering of gene expression data European Bioinformatics Institute (EBI) Web
GEDA Gene expression data analysis and simulation tools, offering a variety of options for processing and analyzing results. University of Pittsburgh and UPMC Web
GenMAPP Tools for visualizing data from gene expression experiments in the context of biological pathways. Conklin lab; Gladstone Institute & the UCSF Windows
GeneX Gene Expression Database : integrated toolset for data analysis and comparison National Center for Genome Resources Windows, Linux, SunOS/Solaris
TIGR MultiExperiment Viewer Analysis and Visualization of Microarray Data TIGR JAVA
TreeArrange and Treeps Software for displaying and manipulating hierarchical clustered data University of Waterloo, Canada Linux, Unix, Windows