From Genome Technology Core (GTC) wiki - Sequencing and Microarray
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
|
