MIAME List of
MD Software

Microarray
Software
Comparison

Microarray Software and Databases

SoftwareCategoryDescription
SMDDatabaseStanford
LonghornArray DatabaseDatabaseOK State U
YaleMicroarray DatabaseDatabaseYale
AMADDatabasemicroarrays.org
ArrayExpressDatabaseEBI
caArrayDatabaseNCI
MicroarrayEXPDatabaseUSDA - Soybean
Gene ExpressionOmnibusDatabaseNCBI
UNC Microarray DatabaseDatabaseUniv of N Carolina - Chapel Hill
MaxDDatabaseManchester Bioinformatics
NOMADDatabaseChris Seidel's Lab
MIDASDatabaseSanger
IMADDatabaseIllinois
BASEDatabaseLund University
QuickLIMSDatabaseMS Access version
DAVIDannotationProvides a comprehensive set of tools forinvestigators to visually summarize annotation from large list ofgenes.
dragonhopkinsannotationGeneannotation tool
geneLynxannotationGeneannotation
genetideannotationGeneannotation
globalviewerannotationprovidesa synthetic view of the transcriptional expressionprofiles of yeast genes
karmaannotationArraymanager and annotator
matchminerannotationnablesthe user to translate between disparate ids for the same gene
netaffyxannotationAffymetrixtools for annotation
PantherannotationGeneannotation
RESOURCERER:(TIGR)annotationprovides annotation based on the TIGR GeneIndices (TGI) R
SOURCEannotation
CDFfilesarray informationMicroarrays Data Libraries
chipinfoarray information
CloneTrackerarrayinformationSystem for managing and processing allinformation associated with fabrication of spotted microarrays
ArrayMakerarray makerprovideshigh performance robotic control of microarrayer robots
eXPatGencluster analysisAnOn-line Gene Expression Pattern Generator
ClusteranalysisclusteranalysisOn line software that do unsupervisedClustering
CWTCclusteranalysisA method designed to mine large sets ofmicroarray data. The basic idea is to perform two kinds of clusteranalysis;
fclusterclusteranalysisSoftware for fuzzy clustering
FreeViewclusteranalysisAgene dendrogram viewer
FuzzyClusteringclusteranalysisContainswell-known algorithms like the fuzzy c-means algorithm
GHMMcluster analysisMaxPlanck Institute for Molecular Genetics, Department of ComputationalMolecular Biology, University of Cologne
GIMMcluster analysisA clustering procedure based on theconcept of Bayesian model-averaging and a precise statistical model ofexpression data
GQLclusteranalysisA GHMM-based tool for querying andclustering Gene-Expression time-course data)
HeatMapBuilderclusteranalysisGenerates customizable heatmaps frommicroarray data
lexcavatorcluster analysisasoftware tool used for gene expression data clustering.EXCAVATOR can run on any platform with the Unix or Linux operatingsystem.
MCVEclusteranalysisA cluster validity tool for geneexpression data
pagecluster analysisTool to attach expression pattern to genesrepresented in a collection of hybridization array experiments
QuantumClusteringcluster analysis
SOTAclusteranalysisOn line software that do Clustering(calculus and graphics)
svmlightclusteranalysisThis software does SVM (Clustering)
TreeArrangeand TreepsclusteranalysisTool for displaying expression array dataand optional associated heirarchial clustering in the form ofencapsulated postscript files
TreeViewclusteranalysisGraphically browse results of clusteringand other analyses from Cluster
XClusterclusteranalysisPerform hierarchical clustering,self-organizing maps
expressionanalysiscustom analysisSpecializinginmicroarray analysis,bioinformatics, and expression gene profiling service.
MicroarrayData Assemblerdata assmeblyExcel-basedsoftware developed by Anbazhagan Ramaswamy forassembling microarray data
biogopherdata integrationfacilitatesthe integration of your local bioinformatics data with public datasources
MAPSdata integrationSystem for management and interpretationof microarray gene expression experiment information and data
Microhelperdata integrationfor merging datasets, checking dataintegrity, filtering noises, and normalizing data
ondexdata integrationEnables data from diverse biological data sets to be linked, integrated andvisualised
ACIDdatabaseadatabase for microarray clone information
BASEdatabaseA comprehensive database server to managethe massive amounts of data generated by microarray analysis.
gominergene ontologyatool for biological interpretation of 'omic' data
GO-TermFindergene ontologyFinds GO terms significantly associatedwith a list of genes
OntologyTraversergene ontologyGOsearch using R
SparseLOGREGgene selectionIt makes use of LTI-Lib and the PythonImaging Library. I
AbleImage Analyserimage analysissupports image analysis functions thatinclude dimensional, gray scale and 24 bits color measurements.
ArrayFoximage analysisAutomatic detection of background noiseand contaminations.
Array-Proimage analysisA tool for the nascent microarray andhigh-throughput screening research efforts fueling the genomics,proteomics, drug discovery and bioinfor
ArrayVisionimage analysisA flexible software package for thequantification of gene expression and protein arrays.
Dappleimage analysisA program for quantitating spots on atwo-color DNA microarray image.
GenePixProimage analysisBatch Analysis tab for browsing andanalyzing batches of images
GridGrinderimage analysisOffers industrial strength image analysisfeatures for microarrays
Iconoclustimage analysisA powerfulimaging software for the analysis of array images of multipleformats.
ImaGeneimage analysisimageanalysis
Koadarrayimage analysisimageanalysis
MACROviewimage analysisAnalyzes microarray images in TIFF formatthat are generated by microarray scanners
MicroVigeneimage analysisIncludes many features and functions thatwill facilitatemicroarray images.
MicroVigeneimage analysisimageanalysis
PhoretixArrayimage analysisimageanalysis
QuantArrayimage analysisimageanalysis
ScanAlyzeimage analysisimageanalysis
SensiChipViewimage analysisAn image analysis software package focusedto allow streamlined and intuitive image and data evaluation andproceding
Spatter:(Savannah)image analysisA software package which performs DNAmicroarray image analysis.er, and does not require any user interactionwhile it runs.
Spotimage analysisimageanalysis
SpotReaderimage analysisimageanalysis
Cytoscapenetwork visualizationVisualizemolecular interaction
Pajek:Large Network Analysisnetwork visualization 
Relnetnetwork visualizationconstructrelevance networks from their gene expression data.
ArrayplotnormalizationNormalisation software, with somevisalisation tools
SNOMADnormalizationStandardization and Normalization of MicroArray Data
BAGELpathwayanalysisBayesianAnalysis of Gene Expression Levels: a program for the statisticalanalysis of spotted microarray data.
GenMAPPpathwayanalysisTools for visualizing data from geneexpression experiments in the context of biological pathways.
MGraphpathway analysisGraphicalmodels for microarray data analysis
ArrayDesignerprimer designTool assisting in primer design formicroarray construction
arrayExpressrepositorypublicrepository for microarray data
princetondbrepository
ArrayStatstatistical packageA unique statistical package that has beendesigned for analysis of microarray gene expression data
BAGELstatisticalpackageBayesian Analysis of Gene ExpressionLevels: a program for the statistical analysis of spotted microarraydata.
BAMarraystatisticalpackageBayesian Analysis of Variance forMicroarrays - detect differentially expressed genes from multigroupmicroarray data
ChipST2CstatisticalpackageHCA, K-means cluster analysis, T-test,Mann-Whitney, F-test, Kruskal-Wallis, Significant genes listed in Excelspreadsheets.
CLUSFAVORstatisticalpackageunsupervised hierarchical cluster andprincipal component analyses of DNA microarray transcriptional profiles.
CyberTstatisticalpackaget-test for statistically significantdifferences between sample sets for arrays;
DTREGstatisticalpackageApowerful statistical analysis program
GeneMathsstatistical packagetools fortime-course experiments
GLRstatisticalpackageA statistical analysis program toidentifydifferentially expressed genes from microarray data.
iGEAstatistical packageForuse from the Windows command line
KNNimputestatisticalpackageEstimation of missing microarray values
MA-ANOVAstatistical packageA set of functions written in Matlab forthe analysis of variance on microarray data.
Octavestatistical packageDataanalysis
PAMstatisticalpackagePrediction Analysis for Microarrays
pcatutorialstatistical package
P-scanstatistical packagePeak Quantification using StatisticalComparitive Analysis
RstatisticalpackageA very popular software for statistician.
SAMstatistical packageSignificance Analysis of Microarrays :Supervised learning software for genomic expression data mining
SASstatistical packagestatisticalanalysis
Statisticastatistical packagestatisticalanalysis
SuperPCstatisticalpackageSurvival and regression analysis formicroarrays
VERA& SAMstatisticalpackageFinding significant expression differencesin DNA microarray data
AMIADAsuitean integrated computer program fororganizing, exploring, visualizing, and analyzing microarray data
ANOVAToolsuiteNIAArray Analysis tool
AppliedMathssuitesoftware
ArrayMiner®suiteA set of analysis tools using advancedalgorithms to reveal the true structure of your microarray data.
ArrayPacksuiteOffers a suite of applications whichmanages all three parts of array expression projects.
arraypipesuiteA Flexible Processing Pipeline for Microarray Data
arraytracksuiteMicroarraysuite
BioConductorsuiteAn open source software for analyzinggenomic data,especially microarray data
BioDiscoverysuiteImage analysis, data management and tracking and data analysis software(Windows 95/98/NT4).
BRBarray toolssuiteAn integrated package for thevisualization and statistical analysis of microarray gene expressiondata. T
CAGEDsuiteBased on amethod called Bayesian Clustering by Dynamics,
cagedasuiteA free, open-source, collaborative onlinegene expression data analysis web application
DAMAsuiteMicroarrayservice
dChipsuiteLow-level and high-level analysis ofoligonucleotide microarrays
EBItoolssuitemicroarraytool collection
engenesuiteAnalysis tools for visualizing, pre-processing and clustering microarrayexpression data
EnodarsuiteVendor
expressyourselfsuiteMicroarraydata processing platform
ExpressionProfilersuiteA set oftools for clustering, analysis and visualization of gene expression andother genomic data. T sequences, study protein interactions, as well asto link analysis results to external tools and databases.
ExpressionistsuiteAnalysistools
ExpressionSievesuiteMicroarray data analysis package, strongin linking biological significance to expression patterns,
GAASsuiteAn integrated software framework forefficient management, analysis and visualization of large amounts ofgene expression data
GCOSsuiteMicroarray suite
GEDAsuiteGeneExpression Data Analysis Tool
genepatternsuiteSupervised classification, gene selectionand permutation test methods.
genepublishersuiteperformsautomated data analysis
GeneSiftersuiteCombines data management and analysis tools.
GeneDirectorsuiteacomprehensive microarray data management solution
geneGobisuiteexploratoryanalysis of microarray data and metabolic networks
GeneLinkersuiteGene expression and proteomics analysis software.
GenePatternsuiteapowerful analysis workflow tool
GenePilotsuiteApowerful and intuitive MicroArray Analysis tool
GenePublishersuitePerform automated data analysis from geneexpression experiments on a number of different platforms.
GeneSiftersuiteAccess to powerful statistical toolsthrough a web interface, with integrated features for determining thebiological significance of the data.
GeneSightsuiteMicroarray suite
GenesissuiteMicroarraysuite
GeneSpringsuiteAn analytical workbench for microarraydata analysis that enables visualization, organization and manipulationof gene expression data
GeneXsuitea client application that provides aninterface to a relational database managment system
GeneXplorersuiteGene Expression Database : integratedtoolset for data analysis and comparison
GeneXPresssuiteMicroarraysuite
GenMathssuiteAnalysis of high density microarrays andgene chips
Genowiz™suiteA Gene Expression Data Analysis andManagement Tool.
GEPASsuiteA collection of tools for complete dataanalysis
GEPSsuiteprovides interactive pattern analysis
gfindersuiteGenome Function INtegrated Discoverer
GSEAsuiteGene set enrichment analysis
IBMgene workssuitea softwarepackage toanalyze patterns in gene array chip data.
INCLUSivesuiteINCLUSive(INtegrated CLustering, Upstream Sequence retrieval and motif)
J-ExpressPro: (MolMine)suitea comprehensive portable software package
LACKsuiteCharles C Kim & Stanley Falkow,Stanford University
limmasuiteABioconductor module
MAExplorersuiteAnalyzed microarray data in specific steps.
Matarraysuiteaset of Matlab tools designed for the analysis of microarray data.
matlabtoolboxsuiteprovidesseveral methods for analysis
mchipssuiteintegratedwith a software platform for microarray data analysis
MIDASsuiteDataanalysis
NIAMicroarray ANOVA ToolsuiteDataanalysis
OntoToolssuiteSoftwaresuite
orangecanvassuite
Parteksuite
PARTISANarrayLIMSsuite
RACEsuite
RosettasuiteArraymanager and annotator
ScoreGenessuite
SeqExpresssuite
SilicoCytesuiteAn advanced, modular, flexible and highlyintegrated microarray analysis platform
SMDsuiteMicroarray suite
SpotfireProsuiteSpotfire Pro from Spotfire, Inc.
STEMsuiteAJava program for clustering, comparing,and visualizing short time series gene expression data (
SVDMANsuiteProgram for Singular Value DecompositionAnalysis of global gene expression data
TableViewsuiteCenter for Computational GenomicsandBioinformatics, University of Minnesota
THEAsuitesuite
TIAMDsuiteMicroarray suite
VampiresuiteMicroarray suite
VextorXpressionsuiteNormalization, Filtering, sorting,clustering algorithms
CaryoScopevisualizationViewing aCGH or expression data in awhole-genome context.
ciMinervisualizationgeneratescolor-coded Clustered Image Maps to representgene expression profiles
Cleaver1.0visualizationProvides a variety of tools to assist inthe analysis of microarray expression data. I
ClustervisualizationFromEisenÂ’s lab
Cluster3.0visualizationPerform hierarchical clustering,self-organizing maps
F-scanvisualizationF-scan For the two channels of an image,generate a file containing spot intensities and addresses and display ascatterplot. Compare spot intensities between the red and greenchannels and generate a list of over and under expressed genes.Visually examine pairs of spots reported as differentially expressed.
JavaTreeviewvisualizationView Results of Clustering
OmniVizvisualizationDatavisulaization
pcasvdvisualization
slcviewvisualizationViewResults of Clustering
VennMappervisualizationSmid M, Dorssers LC, Jenster G.Departmentof Pathology, Josephine Nefkens Institute. The Netherlands.


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