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Created on: 12-Oct-2012   Last updated on: 12-Oct-2012  |  How to cite this?
Total resources - 157
A list of resources for microarray data analysis
Akhilesh Bajpai and Sravanthi Davuluri (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources
Short description*Rank by usage frequency Click to Edit / Add comments
Bioconductor - Open source software for Bioinformatics
http://www.bioconductor.org
Provides tools for the analysis and comprehension of high-throughput genomic data
36
Cluster
http://rana.lbl.gov/EisenSoftware.htm
Cluster analysis (Hierarchical clustering, SOMs, k-means, PCA) of microarray gene expression datasets
50

URL not working as on 15 Nov 2016
BASE - BioArray Software Environment
http://base.thep.lu.se
Data analysis, information and management system for microarray data
58
AMP - Automated Microarray Pipeline
http://www.tm4.org/amp.html
A web-based application for Affymetrix microarray data normalization and statistical analysis
77

URL not working as on 15 Nov 2016
BRB ArrayTools
http://linus.nci.nih.gov/BRB-ArrayTools.html
Integrated package for statistical analysis and visualization of microarray gene expression data
96
CIT - Cluster Identification Tool
http://www.vai.org/vari/bioinformatics.htm
A data analysis program that identifies differentially expressed clusters of genes from microarray data
98

URL not working as on 2 Feb 2015 (confirmed on 15 Nov 2016)
CAGED - Cluster Analysis of Gene Expression Dynamics
http://dcommon.bu.edu/xmlui/handle/2144/1290
A program for analysis of temporal gene expression data
99
dChip - DNA-Chip Analyzer
http://www.hsph.harvard.edu/cli/complab/dchip/
A software package for gene expression and SNP microarray data analysis and visualization
99
2HAPI - version 2 of High density Array Pattern Interpreter
http://array.sdsc.edu
A web-based tool for microarray data analysis including searching, manipulating, visualizing, and clustering
100

URL not working as on 2 Feb 2015 (confirmed on 15 Nov 2016)
Affymate
http://www.arraygenetics.com/about_arrayQuest.php3?#am
Data analysis program for Affymetrix gene chips
100

URL not working as on 2 Feb 2015 (confirmed on 15 Nov 2016)
AIDA array
http://www.raytest.de/bio_imaging/products/aida/arrayevaluation/products_aida_arrayevaluation.html
Microarray image analysis software
100
AMADA
http://web.hku.hk/~xxia/software/AMADA.htm
Tool for data transformation, clustering, derivation of co-expressed genes and visualizations
100

URL not working as on 2 Feb 2015 (confirmed on 15 Nov 2016)
A-MADMAN - Annotation-based MicroArray DataMeta ANalysis tool
http://compgen.bio.unipd.it/bioinfo/amadman
Annotation based meta-analysis of data from NCBI GEO
100
AMDA - Automated Microarray Data Analysis
http://sourceforge.net/projects/automicroarray
A cross-platform microarray data analysis tool for Affymetrix gene/exon arrays, 3 prime IVT arrays, Illumina Bead arrays, and one-channel Agilent 444 arrays
100
AMIA - Automated Microarray Image Analysis Toolbox for MATLAB
http://www.pnl.gov/statistics/amia
Image analysis tool for extracting microarray spot profiles from microarray images
100
AMIADA - Analysing MIcroArray Data
http://dambe.bio.uottawa.ca/amiada.asp
An integrated program for organizing, exploring, visualizing, and analyzing microarray data
100
ARMADA - Automated Robust Microarray Data Analysis
http://www.grissom.gr/armada
A MATLAB implemented program which performs all steps of typical microarray data analysis including filtering, background correction, normalization, statistical analysis, clustering and visualization
100
ArrayFox
http://www.imaxia.com/products.htm
Software for automated quantification of microarray images
100

URL not working as on 2 Feb 2015 (confirmed on 15 Nov 2016)
ArrayLeaRNA
http://www.ifr.ac.uk/safety/ArrayLeaRNA
A novel Bayesian approach, available as excel add-in for analyzing microarray expression data
100
ArrayMiner - Powerful analysis tool for your microarray gene expression data
http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm
Analysis and visualization of microarray gene expression data
100
ArrayMining - Online Microarray Data Mining
http://www.arraymining.net
A web-application for microarray analysis including feature selection, clustering, prediction, gene set analysis and cross-study normalization
100
ArrayOU
http://www.bioinformatics.plantbio.ohiou.edu
A web-based tool for analysis and visualization of data from commercially available and customized Agilent expression microarrays, and can be extended for further implementations
100
ArrayPipe
http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl
Analysis and visualization of two-color microarray data
100
Arrayplot
http://www.transcriptome.ens.fr/arrayplot
Software for normalization and visualization of microarray data
100
Array-Pro Analyzer - Microarray analysis software for fast, accurate and repeatable results
http://www.mediacy.com/index.aspx?page=ArrayPro
Array image analysis software
100
ArrayQuest - An online DNA microarray analysis system
http://proteogenomics.musc.edu/arrayquest
Tool to analyze data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or own data
100
arraySCOUT
http://www.lionbioscience.com/solutions/arrayscout
Analysis of gene expression data from different microarray platforms
100

URL not working as on 2 Feb 2015 (confirmed on 15 Nov 2016)
ArrayTrack
http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack
A database, data analysis & interpretation tool
100
ArrayVision
http://www.biocompare.com/Product-Reviews/41169-ArrayVision-Version-8-0/
Data analysis and visualization software
100
Asterias
http://asterias.bioinfo.cnio.es
Applications for high-throughput genomic data analysis including normalization, filtering, differential gene expression, class and survival prediction model building
100
AVA - Array Visual Analyzer
Available upon request: yihua-zhou2@monsanto.com
A Java program for visualization and analysis of gene expression microarray data
100

The software is freely available for academic users on request from the authors- yihua-zhou2@monsanto.com
Babelomics
http://www.babelomics.org
Suite of web tools for high-throughput data analysis including microarray and functional annotations
100
BAGEL - Bayesian Analysis of Gene Expression Levels
http://en.bio-soft.net/chip/BAGEL.html
Statistical analysis of differential gene expression between two or more samples measured on two-channel microarrays
100
BAMarray - Bayesian Analysis of Variance for Microarrays
http://www.bamarray.com
Statistical technique for detecting differentially expressed genes
100
BicOverlapper
http://vis.usal.es/bicoverlapper
Biclustering of gene expression data
100
BioMine
http://www.gnsbiotech.com/biomine.shtml
An integrated application for gene expression microarray data analysis
100
BiVisu
http://www.eie.polyu.edu.hk/~nflaw/Biclustering
Detection of biclusters and their visualizations
100
BxArrays - Online Microarray Data Analysis
http://bioinforx.com/lims/microarray-gene-expression-data-analysis/bxarrays
A web-based microarray data management and analysis system for major platforms, including Affymetrix, Agilent, NimbleGen, and more
100
CARMAweb - Comprehensive R based Microarray Analysis web frontend
https://carmaweb.genome.tugraz.at/carma
A data analysis web service based on R and Bioconductor software packages
100
Caryoscope
http://caryoscope.stanford.edu
A Java based application for visualizing array comparative genome hybridization microarray data
100

URL not working as on 3 Feb 2015 (confirmed on 15 Nov 2016)
CGcgh
http://www.mcu.edu.tw/department/biotec/en_page/CGcgh
A MATLAB-based, array comparative genomic hybridization data analysis program
100
CGH explorer
http://www.ifi.uio.no/bioinf/Papers/CGH
A program for statistical analysis and visualization of microarray-based comparative genomic hybridization data
100
CGH plotter
http://sigwww.cs.tut.fi/TICSP/CGH-Plotter
A MATLAB toolbox with a graphical user interface to analyze comparative genomic hybridization microarray data
100

URL not working as on 3 Feb 2015 (confirmed on 15 Nov 2016)
CGHnormaliter
http://bioconductor.org/packages/2.6/bioc/html/CGHnormaliter.html
A software for normalization of array CGH data with imbalanced aberrations
100
CGHweb - Enabling users to analyze their array-CGH data with multiple algorithms simultaneously
http://compbio.med.harvard.edu/CGHweb
Analysis of array-CGH data with multiple algorithms simultaneously
100
ChipInspector
http://en.bio-soft.net/chip/ChipInspector.html
Microarray data analysis tool
100
ChipST2C
http://www.chipst2c.org
Significance testing to cluster analysis of microarray data
100

URL not working as on 3 Feb 2015 (confirmed on 15 Nov 2016)
Chipster - Open source platform for data analysis
http://chipster.csc.fi
A data analysis tool for next generation sequencing, microarray and proteomics data
100
Cleaver - Classification of Expression Array Version
http://classify.stanford.edu
Provides tools for visualization, classification, and clustering of microarray expression data
100
CLIC - Clustering analysis of Large microarray data with Individual dimension-based clustering
http://gexp2.kaist.ac.kr/clic
Clustering analysis with individual dimension-based clustering
100
CLUSFAVOR - CLUSter and Factor Analysis with Varimax Orthogonal Rotation
http://mbcr.bcm.tmc.edu/genepi
Software program for hierarchical cluster and principal-component analysis of microarray gene expression data
100

URL not working as on 3 Feb 2015 (confirmed on 15 Nov 2016)
ClustArray
http://www.cbs.dtu.dk/services/DNAarray
Clustering and annotated visualization of the microarray gene expression data
100

Website states that the software is no longer available as a web server but it can be obtained by sending an email to Christopher Workman: workman@cbs.dtu.dk
CRCView
http://helab.bioinformatics.med.umich.edu/crcview
A web server for model-based clustering of microarray gene expression data
100
Cyber-T
http://cybert.ics.uci.edu
Differential analysis of DNA and protein microarrays, next generation sequencing and mass spectrometry data
100
daMA - Efficient design and analysis of factorial two-colour microarray data
http://www.bioconductor.org/packages/2.10/bioc/html/daMA.html
Tool for the design and statistical analysis of factorial two color microarray data
100
Dapple
http://www1.cse.wustl.edu/~jbuhler/dapple
Microarray image processing software
100
DetectiV - Analysis of pathogen detection microarray data
http://detectiv.sourceforge.net
Tool for visualization, normalization and significance testing of pathogen detection microarray data
100
DNMAD - Diagnosis and Normalization of MicroArray Data
http://dnmad.bioinfo.cnio.es
A web server for quality assessment and normalization of cDNA microarray expression data
100
EAA - Exon Array Analyzer
http://eaa.mpi-bn.mpg.de
Software to analyze Affymetrix GeneChip, Exon 1.0 ST Arrays to identify alternative splicing
100
EBarrays - Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
http://www.bioconductor.org/packages/release/bioc/html/EBarrays.html
Tools for the analysis of microarray data
100
EB-HMM - Microarray Time Course Analysis
http://www.biostat.wisc.edu/~kendzior/EB-HMM
Identification of differentially expressed genes across multiple conditions over time
100
EDGE(3)
http://edge.oncology.wisc.edu
An open-source, web-based application for the storage, analysis, and sharing of Agilent two color microarray experiments
100

URL not working as on 4 Feb 2015 (confirmed on 15 Nov 2016)
EMA - Easy Microarray data Analysis
http://bioinfo.curie.fr/projects/ema
A software based on R functions for the analysis and visualization of Affymetrix expression microarray data
100
EMMA
http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info
A platform that gives access to all the microarray data sets stored in the ArrayLIMS and provides automated pipelines for data processing
100
Engene - Gene-Expression Data Processing and Exploratory Data Analysis
https://chirimoyo.ac.uma.es/engenet
Tool for storing, visualizing and processing large scale gene expression data
100
EXPANDER - EXPression ANalyzer and DisplayER
http://acgt.cs.tau.ac.il/expander
Tool for data analysis and annotation of microarray gene expression data
100
Expressionist
http://www.genedata.com/products/expressionist
Software for omics data management
100
ExpressionSieve
http://www.biosieve.com/product.html
Data analysis, data mining and visualization software from BioSieve
100

URL not working as on 4 Feb 2015 (confirmed on 15 Nov 2016)
ExpressYourself - Microarray data processing platform
http://array.mbb.yale.edu/analysis
Microarray data analysis platform
100
EzArray
http://ezarray.com
A web-based system for Affymetrix expression array data management and analysis
100

Website recommends the use of BxArrays as EzArray is not functioning due to changes on the GEO website and R/Bioconductor packages (as on 15 Nov 2016)
Freeview & FreeOView
http://www.biolab.si/app/freeview
Programs for visualization and optimization of gene expression dendrograms
100
fRMA - Frozen Robust Multiarray Analysis
http://bioconductor.org/packages/release/bioc/html/frma.html
A software for preprocessing and analysis of single microarrays and microarray batches
100
F-SCAN - Fluorescently Probed cDNA Microarray Analysis
http://abs.cit.nih.gov/fscan
Tool for image processing and data normalization of two channel cDNA microarrays
100
GAA - Gene Array Analyzer
http://gaa.mpi-bn.mpg.de
Software to analyze Affymetrix GeneChip, Gene 1.0 ST Arrays to identify alternative splicing
100
GAAS - Gene Array Analyzer Software
http://www.medinfopoli.polimi.it/GAAS
An integrated software for management, analysis and visualization of microarray gene expression data across replicated experiments
100
GEDA - Gene Expression Data analysis
http://bioinformatics.upmc.edu/GE2/GEDA.html
Microarray gene expression data analysis tool
100

URL not working as on 4 Feb 2015 (confirmed on 15 Nov 2016)
GEMS - Gene Expression Module Sampler
http://genomics10.bu.edu/terrence/gems
Biclustering of gene expression data
100
Gene Cluster
http://nf.nci.org.au/facilities/software/software.php?software=Gene+Cluster
Clustering analysis (Hierarchical clustering, k-means and k-medians clustering, and 2D SOMs) tool
100
GeneClust
http://odin.mdacc.tmc.edu/~kim/geneclust
Clustering analysis (Hierarchical clustering and Gene shaving) tool
100
GeneLinker Gold
http://www.lifescisoft.com/genelinker-gold.html
Data analysis tool including normalization, filtering, clustering, and visualizations of microarray data
100
GeneMaths XT
http://www.applied-maths.com/ge/ge.htm
Data analysis software
100
GenePattern
http://www.broad.mit.edu/cancer/software/genepattern
Tools for gene expression analysis, proteomics, SNP analysis, flow cytometry and RNA-seq analysis
100
GenePix Pro
http://www.moleculardevices.com/Products/Software/GenePix-Pro.html
A standalone microarray image analysis software from Molecular Devices
100
GenePublisher
http://www.cbs.dtu.dk/services/GenePublisher
Data analysis of microarray data from various platforms
100
GeneSifter
http://www.genesifter.net
Data analysis tool for microarray and NGS platforms
100
Genesis
http://genome.tugraz.at/genesisclient/genesisclient_description.shtml
A Java based tool for normalization, visualization, clustering and gene to chromosomal mapping
100
GeneSpring
http://www.strandls.com/GeneSpring
A commercial tool for microarray data analysis and visualization
100
GeneTraffic
http://142.150.9.81
Data analysis software for two channel microarrays
100

URL not working as on 4 Feb 2015 (confirmed on 15 Nov 2016)
GeneWeaver
http://www.visual-bioinformatics.com/geneweaver_overview.asp
Gene expression data analysis software for microarray, EST and SAGE based experiments
100

URL not working as on 6 Feb 2015 (confirmed on 15 Nov 2016)
Genom
http://en.bio-soft.net/chip/genom.html
Gene expression array data analysis and functional annotation tool
100
Genowiz
http://www.ocimumbio.com/genowiz/
Data analysis software to store, process and visualize gene expression microarray data
100
GEOSS - Gene Expression Open Source System (previously known as GeneX Va)
http://va-genex.sourceforge.net
A complete system to store and analyze gene expression data with integrated database and analysis suite
100
GEPAT - Genome Expression Pathway Analysis Tool
http://gepat.sourceforge.net/index.htm
A gene expression microarray data analysis tool with features for data normalization, clustering, visualization and data interpretation using functional annotations and pathway information
100
Ginkgo - CGH and Expression Microarray Statistical Analysis and Normalization Platform
http://pfgrc.jcvi.org/index.php/bioinformatics/ginkgo.html
Data analysis platform for CGH and gene expression microarrays
100
GLR
http://www.cc.utah.edu/~jw27c60
A statistical analysis program to identify differentially expressed genes from microarray data by implementing a generalized likelihood ratio test
100
GLR
http://en.bio-soft.net/chip/glr.html
A statistical analysis tool for microarray data
100
iArray - Integrative Array Analyzer
http://zhoulab.usc.edu/iArrayAnalyzer.htm
A data mining and visualization tool for integrative analysis of multiple cross platform microarray datasets
100
Iconoclust
http://iconoclust.software.informer.com/
Microarray image analysis software
100
ImaGene
http://www.biodiscovery.com/software/imagene
Microarray data analysis software from BioDiscovery
100
IPLab
http://www.spectraservices.com/IPLAB.html
A software for image analysis, processing and measurement of comparative genomic hybridization arrays, in-situ hybridization and co-localization experiments
100
J-Express - Gene expression analysis software
http://jexpress.bioinfo.no
Gene expression array analysis tool
100
Koadarray
http://www.koada.com/koadarray
A software for microarray image analysis and quantification
100
LIMMA - Linear Models for Microarray Data
http://bioinf.wehi.edu.au/limma/index.html  http://www.bioconductor.org/packages/release/bioc/html/limma.html 
A software package for the analysis of gene expression microarray data
100
M2DB - Microarray Meta-analysis DataBase for human clinical studies
http://metadb.bmes.nthu.edu.tw/m2db/Index.html
A curated database and analysis software for two Affymetrix platforms (Human U133A and Human U133 plus 2.0)
100
MA2C - Model-based Analysis of 2-Color Arrays
http://liulab.dfci.harvard.edu/MA2C/MA2C.htm
Normalization method based on the GC content of probes for two-color tiling-arrays
100
MAANOVA - Tools for analyzing Micro Array experiments
http://www.bioconductor.org/packages/2.10/bioc/html/maanova.html
A software package for statistical analysis of gene expression data from two-color cDNA microarray experiments
100
MACGT - Multi-dimensional Automated Clustering Genotyping Tool
http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml
A Java application that can cluster complex multi-dimensional vector data derived from single nucleotide polymorphism genotyping experiments
100

URL not working as on 6 Feb 2015 (confirmed on 15 Nov 2016)
Machaon CVE - Clustering and Validation Environment
http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html
A cluster validation tool for gene expression data
100

URL not working as on 6 Feb 2015 (confirmed on 15 Nov 2016)
MAExplorer - Microarray Explorer
http://www.lecb.ncifcrf.gov/MAExplorer
Microarray data analysis software
100
MAGIC Tool - MicroArray Genome Imaging and Clustering Tool
http://www.bio.davidson.edu/MAGIC
Microarray image and data analysis software
100

Magnolia - Microarray Data Management and Export System for PFGRC Microarrays
http://pfgrc.jcvi.org/index.php/bioinformatics/magnolia.html
Data storage system for experimental parameters, source, sample, probe, slide, scan, expression, and normalization method of microarray experiments
100
MAIA - Microarray Image Analysis
http://bioinfo.curie.fr/projects/maia
Image analysis software for cDNA, array CGH and protein microarrays
100
MARS - Microarray Analysis and Retrieval System
http://genome.tugraz.at/mars/mars_description.shtml  https://mars.genome.tugraz.at/marsWEB 
A comprehensive MIAME compliant suite for storing, retrieving, and analyzing multi color microarray data
100
MatArray
http://www.ulb.ac.be//medecine/iribhm/microarray/toolbox
A set of MATLAB tools for microarray data analysis including normalization and clustering
100
Mayday
http://en.bio-soft.net/chip/mayday.html
Analysis, visualization and storage of microarray data
100
MCGH
http://folk.uio.no/junbaiw/mcgh
A MATLAB toolbox with graphical interface for the analysis of microarray-based comparative genomic hybridization data
100
M-CHiPS - Multi-Conditional Hybridization Intensity Processing System
http://www.dkfz.de/mchips
A microarray data warehouse integrated with a software platform for data analysis
100

URL not working as on 6 Feb 2015 (confirmed on 15 Nov 2016)
MeV - MultiExperiment Viewer
http://en.bio-soft.net/chip/MeV.html
A Java based application for microarray data processing, visualization and statistical analysis
100
Microarray R US
http://norris.usc.libguides.com/MicroarrayRUS
An R-based program that integrates widely used Bioconductor packages to perform microarray expression data analysis
100
MicroHelper
http://www.changbioscience.com/microhelperinfo.html
Microarray data analysis tool for normalization, merging, filtering
100
MIDAS - Microarray Data Analysis System
http://en.bio-soft.net/chip/MIDAS.html
Microarray data normalization and filtering tool
100
MIDAW - MIcroarray Data Analysis Web tool
http://midaw.cribi.unipd.it/dnachip
A web tool for the analysis of microarray data including normalization, filtering, visualization and statistical analysis
100

URL not working as on 6 Feb 2015 (confirmed on 15 Nov 2016)
Multi microarray normalisation
http://genome1.beatson.gla.ac.uk/Rweb/anova.html
ANOVA based normalization of dye-swapped experiments
100
MULTI-K
http://mk.nims.re.kr/pub
A cluster-number-based ensemble clustering algorithm, for microarray sample classification
100

URL not working as on 6 Feb 2015 (confirmed on 15 Nov 2016)
NIA Array Analysis tool
http://lgsun.grc.nia.nih.gov/ANOVA
Statistical analysis and visualization of the gene expression microarray data
100
PAM - Prediction Analysis for Microarrays
http://www-stat.stanford.edu/~tibs/PAM
A tool for classification of samples based on microarray gene expression, protein expression and SNP data
100
ParaSAM
http://en.bio-soft.net/chip/parasam.html
An application for significance analysis of microarrays
100
PermutMatrix
http://www.lirmm.fr/~caraux/PermutMatrix
Performs cluster and seriation analysis on microarray gene expression dataset
100
Phoretix Array3
http://pavelvodrazka.tripod.com/www_phoretix_com/array3.htm
Tool for spot identification, quantization and normalization of microarray data
100
Qlucore
http://www.qlucore.com
Tool for analysis of data from microarray, SNP, RNA-seq, real-time PCR, DNA methylation, protein expression technologies
100
R cluster
http://genomics.biochem.uci.edu/cgi-bin/genex/rcluster/index.cgi
A collection of clustering algorithms written in the R language to analyze gene expression experiment
100
RACE - Remote Analysis Computation for gene Expression data
http://race.unil.ch
A suite with collection of web tools for microarray gene expression data analysis
100
RealSpot
http://www.lungmicroarray.org
A software package, to validate the results from DNA microarray data analysis by directly associating spot quality and data with spot images
100

The given URL directs to a webpage, which states that the domain name (lungmicroarray.org) without content is available for sale by its owner through Sedo Domain Marketplace (as on 15 Nov 2016)
RobiNA
http://mapman.gabipd.org/web/guest/robin
An open source software for the analysis of microarray and RNA-seq data
100
SAM - Significance Analysis of Microarrays
http://www-stat.stanford.edu/~tibs/SAM/index.html
Statistical analysis software for expression microarray, protein expression, SNP chip and RNA-seq data
100
ScanAlyze
http://www.eisenlab.org/eisen/?page_id=41
Microarray image analysis tool
100
SeqExpress
http://www.seqexpress.com
A stand-alone desktop application for analysis and visualization of microarray or SAGE data
100
SNOMAD - Standardization and NOrmalization of MicroArray Data
http://pevsnerlab.kennedykrieger.org/snomad.php
A collection of algorithms written in R-language for normalization and standardization of DNA microarray data
100
SNP Filter Scripts
http://pfgrc.jcvi.org/index.php/compare_genomics/snp_scripts.html
A set of scripts for the identification and removal of false positive SNP calls in the raw files from Affymetrix chips
100
Spatter
http://www.nongnu.org/spatter
A command based software package for two-color microarray image analysis
100
Spot
http://www.csiro.au/Organisation-Structure/Divisions/Computational-Informatics/SpotSoftware.aspx
A software package for microarray image analysis
100
Spotfinder
http://www.tm4.org/spotfinder.html
A tool for microarray image processing using the TIFF image files generated by most microarray scanners
100
SpotFire DecisionSite
https://docs.tibco.com/products/tibco-spotfire-decisionsite
A microarray gene expression data analysis tool for normalization, data processing and visualization
100
SpotReader
http://www.nilesscientific.com/overview.nhtml
Microarray image analysis software
100

URL not working as on 6 Feb 2015 (confirmed on 15 Nov 2016)
SpotWhatR
http://blasto.iq.usp.br/~tkoide/SpotWhatR
A microarray data analysis tool based on R statistical language
100
STEM - The Short Time-series Expression Miner
http://www.cs.cmu.edu/~jernst/stem
A Java based program for clustering, comparison, and visualization of short time series gene expression microarray data
100
TableView
http://ccgb.umn.edu/software/java/apps/TableView
A visualization program for various biological data, including EST, SAGE and microarray
100

URL not working as on 6 Feb 2015 (confirmed on 15 Nov 2016)
THEME - Tsing Hua Engine for Microarray Experiment
http://metadb.bmes.nthu.edu.tw/theme
Identification of differentially expressed genes for loop-design microarray experiments
100
TM4 - Microarray software suite
http://www.tm4.org
A suite of software for microarray image analysis, data processing, visualization and data management
100
UCSF Spot
http://en.bio-soft.net/chip/UCSFSpot.html
Microarray image quantification software
100
VAMPIRE
http://sasquatch.ucsd.edu/vampire
An integrated environment for microarray data analysis
100
Vector Xpression
http://register.informaxinc.com/solutions/xpression/main.html
A software with integrated set of tools for normalization, filtering, sorting and clustering
100
VisHiC
http://biit.cs.ut.ee/vishic
A tool for hierarchical clustering and interpretation of gene expression data
100
VIZARD
http://en.bio-soft.net/chip/vizard.html
A Java based program for analysis and visualization of Affymetrix chip data
100
WebArrayDB - Database & Cross-Platform Analysis
http://www.webarraydb.org/webarray/index.html
A cross platform analysis suite for microarray data analysis
100
WebGimm - Cluster Analysis Server
http://eh3.uc.edu/gimm/webgimm
A Java based web tool for clustering analysis of microarray data and enrichment analysis of the clustering results
100
XCluster
http://www.stanford.edu/group/sherlocklab/cluster.html
A software for hierarchical clustering and self-organizing maps
100
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