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ScanAlyze 2.51 Process fluorescent images of microarrays
TreeView 1.60 Graphically browse results of clustering and other analyses from Cluster
ArrayMaker 2.6 provides high performance robotic control of microarrayer robots
J-Express pro 2012 software package for analysis and visualization of microarray data
MAExplorer Version Java-based data-mining facility for cDNA or oligonucleiotide microarray databases
FreeView & FreeOView programs for viewing and optimizing gene expression dendrograms
dchip 2010.01 DNA-Chip Analyzer (dChip) ( is a Windows software package for probe-level and high-level analysis of Affymetrix gene expression microarrays and SNP microarrays
SAM 4.01 Significance Analysis of Microarrays
BRB-ArrayTools 4.5.0 b1 visualization and statistical analysis of DNA microarray gene expression data
AMIADA 2.0.7 program for organizing, exploring, visualizing, and analyzing microarray data
GalFileGenerator v1.4 Conversion of a file of 96 well plates into a file of 384 well plates, and conversion of a file of 384 well plates into an Axon GenePix Gene Array List file
cluster 3.0 20141007 enhanced version of Cluster
GenePattern 3.9.4 analytic tools for genomic data
GenMAPP-CS 0.2 Gene Map Annotator and Pathway Profiler
MADAM v4.1 primary data entry, tracking, and reporting system.
Spotfinder v3.2.1 multi-channel image analysis tool for microarray images
MIDAS 2.22 a normalization and filtering tool used to process the raw data output from Spotfinder
MeV 4.9 main data analysis and visualization tool for microarray
Java Treeview 1.1.6r4 Viewer for Microarray Data in the PCL or CDT format
EXPANDER 7.0 EXpression Analyzer and DisplayER
OligoArray 2.1.3 a program that computes gene specific oligonucleotides that are free of secondary structure for genome-scale oligonucleotide microarray construction.
BAGEL 4.1.1 Bayesian Analysis of Gene Expression Levels (BAGEL): a program for the statistical analysis of spotted microarray data.
CAGED 1.1 a computer program for the analysis of temporal gene expression data.
GAAS Gene Array Analyzer Software
NIA Array Analysis Tool Statistical analysis is based on the single-factor ANalysis Of VAriance
tools for microarray tools for microarray
UCSF Spot 2.1 a program for microarray image quantification
ArrayMiner 5.3 lite a set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data
Venn Mapper 1.01 a program that compares heterologous microarray data sets, based on the number of common, differentially expressed genes.
MAIA 2.75 Demo Microarray Image Analysis Software ,
MAGIC Tool 2.1 MicroArray Genome Imaging & Clustering Tool.
Array Tools 3.3 Add-In for Microsoft Excel, which is designed to handle the microarray data.
Genom 2005 3.42 application for analysing array-experiments.
Mayday 2.14 A workbench for visualization, analysis and storage of microarray data.
ChipInspector 2.1 software to analysis microarray data.
OligoWiz 2.3.0 Microarray Probe Designer.
ENIGMA 1.1 a software tool to extract gene expression modules from perturbational microarray data
PermutMatrix 1.9.3 Software for gene expression microarray data analysis.
KegArray 1.2.4 Java application for microarray data analysis.
Correlate 1.03 An Excel plug-in that performs sparse canonical correlation analysis.
Picky 2.20 demo Oligo Microarray Design and Analysis
ParaSAM An application for significance analysis of microarrays using a parallelized algorithm.
VIZARD 1.2 A Java program for analysis and visualization of Affymetrix GeneChip? data.
COCAS V2.4 A ChIP-on-chip analysis suite.
ArrayCluster 1.0 Mixed Factors Analysis of Microarray Gene Expression Data.
GProcesser 3.0 – Statistical Analysis of GenePix data.


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