software category description                                            
 eXPatGen  cluster analysis An On-line Gene Expression Pattern Generator
Able Image Analyser image analysis supports image analysis functions that include dimensional, gray scale and 24 bits color measurements.
ACID database a database for microarray clone information
AMIADA suite an integrated computer program for organizing, exploring, visualizing, and analyzing microarray data
ANOVA Tool suite NIA Array Analysis tool
Applied Maths  suite software
Array Designer primer design Tool assisting in primer design for microarray construction
Array Maker array maker provides high performance robotic control of microarrayer robots
arrayExpress repository public repository for microarray data
ArrayFox  image analysis Automatic detection of background noise and contaminations.
ArrayMiner® suite a set of analysis tools using advanced algorithms to reveal the true structure of your microarray data. 
arraypipe suite A Flexible Processing Pipeline for Microarray Data 
Arrayplot normalization Normalisation software, with some visalisation tools
ArrayStat statistical package A unique statistical package that has been designed for analysis of microarray gene expression data 
arraytrack suite Microarray suite
ArrayVision  image analysis A flexible software package for the quantification of gene expression and protein arrays.
BAGEL pathway analysis Bayesian Analysis of Gene Expression Levels: a program for the statistical analysis of spotted microarray data.
BAGEL statistical package Bayesian Analysis of Gene Expression Levels: a program for the statistical analysis of spotted microarray data.
BASE database A comprehensive database server to manage the massive amounts of data generated by microarray analysis. 
BioConductor suite An open source software  for analyzing genomic data, especially microarray data
BioDiscovery  suite Image analysis, data management and tracking and data analysis software (Windows 95/98/NT4). 
biogopher data integration facilitates the integration of your local bioinformatics data with public data sources
BRB array tools suite An integrated package for the visualization and statistical analysis of microarray gene expression data. T
CAGED suite  based on a method called Bayesian Clustering by Dynamics, 
cageda suite A free, open-source, collaborative online gene expression data analysis web application 
CaryoScope visualization Viewing aCGH or expression data in a whole-genome context.
CDF files array information Microarrays Data Libraries
chipinfo array information
ChipST2C statistical package HCA, K-means cluster analysis, T-test, Mann-Whitney, F-test, Kruskal-Wallis, Significant genes listed in Excel spreadsheets.
ciMiner visualization generates color-coded Clustered Image Maps to  represent gene expression profiles
Cleaver 1.0 visualization Provides a variety of tools to assist in the analysis of microarray expression data. I
Cluster visualization From Eisen’s lab
Cluster 3.0 visualization Perform hierarchical clustering, self-organizing maps
Cluster analysis cluster analysis On line software that do unsupervised Clustering
CWTC cluster analysis A method designed to mine large sets of microarray data. The basic idea is to perform two kinds of cluster analysis;
Cytoscape network visualization Visualize molecular interaction
DAMA suite Microarray service
Dapple  image analysis A program for quantitating spots on a two-color DNA microarray image. 
dChip suite Low-level and high-level analysis of oligonucleotide microarrays
dragon hopkins annotation Gene annotation tool
DTREG statistical package A powerful statistical analysis program
EBI tools suite microarray tool collection
engene suite Analysis tools for visualizing, pre-processing and clustering microarray expression data
Enodar  suite Vendor 
express yourself suite Microarray data processing platform
Expression Profiler suite A set of tools for clustering, analysis and visualization of gene expression and other genomic data. T sequences, study protein interactions, as well as to link analysis results to external tools and databases.
expressionanalysis custom analysis  Specializing in microarray analysis, bioinformatics, and expression gene profiling service. 
Expressionist suite Analysis tools
ExpressionSieve suite Microarray data analysis package, strong in linking biological significance to expression patterns, 
fcluster cluster analysis Software for fuzzy clustering
F-scan  visualization F-scan For the two channels of an image, generate a file containing spot intensities and addresses and display a scatterplot. Compare spot intensities between the red and green channels and generate a list of over and under expressed genes. Visually examine pairs of spots reported as differentially expressed.
Fuzzy Clustering cluster analysis Contains well-known algorithms like the fuzzy c-means algorithm
GAAS suite An integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data 
GCOS suite Microarray suite
GEDA suite Gene Expression Data Analysis Tool
gene pattern suite Supervised classification, gene selection and permutation test methods.
gene publisher suite performs automated data analysis
Gene Sifter  suite Combines data management and analysis tools. 
GeneDirector suite a comprehensive microarray data management solution
geneGobi suite exploratory analysis of microarray data and metabolic networks
GeneLinker  suite Gene expression and proteomics analysis software. 
GeneMaths statistical package  tools for time-course experiments
GenePattern suite a powerful analysis workflow tool
GenePilot  suite A powerful and intuitive MicroArray Analysis tool
GenePix Pro  image analysis Batch Analysis tab for browsing and analyzing batches of images
GenePublisher suite Perform automated data analysis from gene expression experiments on a number of different platforms. 
GeneSifter suite Access to powerful statistical tools through a web interface, with integrated features for determining the biological significance of the data. 
GeneSight  suite Microarray suite
Genesis suite Microarray suite
GeneSpring  suite An analytical workbench for microarray data analysis that enables visualization, organization and manipulation of gene expression data
genetide annotation Gene annotation
GeneX suite a client application that provides an interface to a relational database managment system
GeneXplorer suite Gene Expression Database : integrated toolset for data analysis and comparison
GeneXPress suite Microarray suite
GenMAPP pathway analysis Tools for visualizing data from gene expression experiments in the context of biological pathways.
GenMaths suite Analysis of high density microarrays and gene chips
Genowiz™ suite A Gene Expression Data Analysis and Management Tool.
GEPAS suite A collection of tools for complete data analysis
GEPS suite provides interactive pattern analysis 
gfinder suite Genome Function INtegrated Discoverer 
GHMM cluster analysis Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, University of Cologne
GIMM cluster analysis A clustering procedure based on the concept of Bayesian model-averaging and a precise statistical model of expression data
global viewer annotation provides a synthetic view of the transcriptional expression profiles of yeast genes
GLR statistical package A statistical analysis program to identify differentially expressed genes from microarray data.
gominer gene ontology a tool for biological interpretation of 'omic' data
GO-TermFinder gene ontology Finds GO terms significantly associated with a list of genes
GQL cluster analysis A GHMM-based tool for querying and clustering Gene-Expression time-course data)
GSEA suite Gene set enrichment analysis
IBM gene works suite a software package to analyze patterns in gene array chip data.
Iconoclust  image analysis A  powerful imaging software for the analysis of array images of multiple formats. 
iGEA statistical package For use from the Windows command line
ImaGene  image analysis image analysis
INCLUSive suite INCLUSive (INtegrated CLustering, Upstream Sequence retrieval and motif)
Integromics Biomarker Discovery suite microarray data analysis package
Java Treeview visualization View Results of Clustering
J-Express Pro: (MolMine) suite a comprehensive portable software package
karma annotation Array manager and annotator
Koadarray image analysis image analysis
LACK suite Charles C Kim & Stanley Falkow, Stanford University
lexcavator cluster analysis a software tool used for gene expression data clustering. EXCAVATOR can run on any platform with the Unix or Linux operating system.
limma suite A Bioconductor module
MAExplorer  suite Analyzed microarray data in specific steps.
MAPS data integration System for management and interpretation of microarray gene expression experiment information and data
Matarray  suite a set of Matlab tools designed for the analysis of microarray data.
matchminer annotation nables the user to translate between disparate ids for the same gene
matlab toolbox suite provides several methods for analysis
mchips suite integrated with a software platform for microarray data analysis
MCVE cluster analysis A cluster validity tool for gene expression data
MGraph  pathway analysis Graphical models for microarray data analysis
Microhelper data integration for merging datasets, checking data integrity, filtering noises, and normalizing data
MIDAS suite Data analysis
netaffyx annotation Affymetrix tools for annotation
NIA Microarray ANOVA Tool suite Data analysis
Octave statistical package Data analysis
OmniViz  visualization Data visulaization
ondex data integration enables data from diverse biological data sets to be linked, integrated and visualised 
OntoTools suite Software suite
orange canvas suite
page cluster analysis Tool to attach expression pattern to genes represented in a collection of hybridization array experiments
Pajek: Large Network Analysis  network visualization
PAM statistical package Prediction Analysis for Microarrays
Panther  annotation Gene annotation
Partek  suite
PARTISAN arrayLIMS suite
pca svd visualization
Phoretix Array  image analysis image analysis
princeton db repository
P-scan  statistical package Peak Quantification using Statistical Comparitive Analysis
Quantum Clustering cluster analysis
R statistical package A very popular software for statistician. 
RACE suite
Relnet network visualization construct relevance networks from their gene expression data.
Rosetta suite Array manager and annotator
SAM  statistical package Significance Analysis of Microarrays : Supervised learning software for genomic expression data mining
SAS statistical package statistical analysis
ScanAlyze  image analysis image analysis
ScoreGenes suite
SensiChip View  image analysis An image analysis software package focused to allow streamlined and intuitive image and data evaluation and proceding 
SeqExpress  suite
SilicoCyte suite An advanced, modular, flexible and highly integrated microarray analysis platform
slcview visualization View Results of Clustering
SMD suite Microarray suite
SNOMAD  normalization Standardization and NOrmalization of MicroArray Data 
SOURCE annotation
Spatter: (Savannah) image analysis Asoftware package which performs DNA microarray image, and does not require any user interaction while it runs. 
Spot  image analysis image analysis
Spotfire Pro  suite Spotfire Pro from Spotfire, Inc. 
SpotReader  image analysis image analysis
STEM suite AJava program for clustering, comparing, and visualizing short time series gene expression data (
SuperPC statistical package Survival and regression analysis for microarrays
SVDMAN suite Program for Singular Value Decomposition Analysis of global gene expression data
svmlight cluster analysis This software does SVM (Clustering)
TableView suite Center for Computational Genomics and Bioinformatics, University of Minnesota
THEA suite suite
TIAMD suite Microarray suite
TreeArrange and Treeps  cluster analysis Tool for displaying expression array data and optional associated heirarchial clustering in the form of encapsulated postscript files
TreeView cluster analysis Graphically browse results of clustering and other analyses from Cluster
Vampire suite Microarray suite
Venn Mapper visualization Smid M, Dorssers LC, Jenster G. Department of Pathology, Josephine Nefkens Institute. The Netherlands.
VERA & SAM statistical package Finding significant expression differences in DNA microarray data
Vextor Xpression suite Normalization, Filtering, sorting, clustering algorithms
XCluster cluster analysis Perform hierarchical clustering, self-organizing maps