Microarray Data Analysis Tools
A-MADMAN	http://compgen.bio.unipd.it/bioinfo/amadman/	analysis
An Introduction to R	http://cran.at.r-project.org/doc/manuals/R-intro.html	analysis
Babelomics	http://babelomics.bioinfo.cipf.es/	analysis
BAMarray	http://www.bamarray.com/	analysis
Box Plot	http://www.alcula.com/calculators/statistics/box-plot/	analysis
ErmineJ	http://chibi.ubc.ca/ermineJ/	analysis
Exon Array Analyzer - Start	http://eaa.mpi-bn.mpg.de/exon/index.php	analysis
exonminer	http://ae.hgc.jp/exonminer/	analysis
GAA	http://gaa.mpi-bn.mpg.de/	analysis
GSA	http://www-stat.stanford.edu/~tibs/GSA/index.html	Analysis
onechannelGUI	http://www.bioinformatica.unito.it/oneChannelGUI/	Analysis
PaGE - Patters from Gene Expression	http://www.cbil.upenn.edu/PaGE/	Analysis
SAM example	http://pages.pomona.edu/~llh04747/gcat_SAMinfo.htm	Analysis
SAM in Excel	http://transcriptome.ens.fr/sgdb/tools/differential_analysis.php	Analysis
illuminations Box Plotter	http://illuminations.nctm.org/ActivityDetail.aspx?ID=77	Box plotter
Cornet	https://bioinformatics.psb.ugent.be/cornet/versions/cornet3.0/	coexpression
CloneGene ID Converter	http://idconverter.bioinfo.cnio.es/	converte
expressionanalysis	http://www.expressionanalysis.com/	custom analysis
Microhelper	http://www.changbioscience.com/microhelperinfo.html	data integration
ondex	http://ondex.sourceforge.net/	data integration
Gene Set Enrichment Analysis - Broad	http://www.broad.mit.edu/gsea/msigdb/msigdb_index.html	GSEA
GSEA	http://www.broadinstitute.org/gsea/downloads.jsp	GSEA
MSigDB Gene sets	http://www.broad.mit.edu/gsea/msigdb/genesets.jsp	GSEA
ArrayVision	http://www.imagingresearch.com/products/ARV.asp	image analysis
Dapple	http://www.cs.wustl.edu/~jbuhler/research/dapple/	image analysis
GenePix Pro	http://www.moleculardevices.com/pages/software/gn_genepix_pro.html	image analysis
Koadarray	http://www.koada.com/koadarray/	image analysis
Phoretix Array	http://www.phoretix.com/news/press/2002/0901.asp	image analysis
Spatter: (Savannah)	http://savannah.nongnu.org/projects/spatter	image analysis
Cytoscape	http://www.cytoscape.org/	network visualization
Pajek: Large Network Analysis	http://vlado.fmf.uni-lj.si/pub/networks/pajek/	network visualization
SNOMAD	http://pevsnerlab.kennedykrieger.org/snomadinput.html	normalization
ProMAT	https://www.pnnl.gov/statistics/ProMAT/	Protein microarray
Affymetrix - Scientific Publications	http://www.affymetrix.com/publications/index.affx	publications
arrayExpress	http://www.ebi.ac.uk/arrayexpress/	repository
princeton db	http://puma.princeton.edu/	repository
ArrayStat	http://www.imagingresearch.com/products/AST.asp	statistical package
DTREG	http://www.dtreg.com/	statistical package
Octave	http://www.gnu.org/software/octave/	statistical package
PAM	http://www-stat.stanford.edu/~tibs/PAM	statistical package
P-scan	http://abs.cit.nih.gov/pscan/index.html	statistical package
SAM	http://statweb.stanford.edu/~tibs/SAM/index.html	statistical package
VERA & SAM	http://db.systemsbiology.net/software/VERAandSAM/	statistical package
amen	https://sourceforge.net/projects/amen/	Suite
AMIADA	http://dambe.bio.uottawa.ca/amiada.asp	suite
ANOVA Tool	http://lgsun.grc.nia.nih.gov/ANOVA/	suite
Applied Maths	http://www.applied-maths.com/genemaths/genemaths.htm	suite
ArrayMiner®	http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm	suite
ArrayPipe A Microarray Data Processing Pipeline	http://www.pathogenomics.ca/arraypipe/	Suite
BioConductor	http://www.bioconductor.org/	suite
BRB array tools	http://linus.nci.nih.gov/BRB-ArrayTools.html	suite
CAGED	http://genomethods.org/caged/	suite
carmaweb	https://carmaweb.genome.tugraz.at/carma/	suite
chipster	https://chipster.csc.fi/	suite
Discover	https://discover.nci.nih.gov/tools.jsp	suite
DNA Microarray Data Processing	http://db.systemsbiology.net/software/ArrayProcess/index.html	Suite
EBI tools	http://www.ebi.ac.uk/microarray/index.html	suite
Enodar	http://www.enodar.com/	suite
Expander	http://www.cs.tau.ac.il/~rshamir/expander/expander.html	suite
express yourself	http://array.mbb.yale.edu/analysis/	suite
Gene Pattern	https://www.genepattern.org/	Suite
gene publisher	http://www.cbs.dtu.dk/services/GenePublisher/	suite
geneGobi	http://www.ggobi.org/	suite
GeneLinker	http://www.improvedoutcomes.com/products/index.html	suite
GenePilot	http://www.genepilot.com/	suite
Genesis	http://genome.tugraz.at/genesisclient/genesisclient_description.shtml	suite
GeneXplorer	http://search.cpan.org/dist/Microarray-GeneXplorer/	suite
GenMaths	http://www.applied-maths.com/ge/ge.htm	suite
INCLUSive	http://www.esat.kuleuven.ac.be/~dna/Biol/Software.html	suite
LACK	http://falkow.stanford.edu/whatwedo/software/software.html	suite
limma	http://bioinf.wehi.edu.au/limma/index.html	suite
MAExplorer	http://maexplorer.sourceforge.net/	suite
Mayday - Microarray Data Analysis	http://www-ps.informatik.uni-tuebingen.de/mayday/wp/	Suite
microarray pipelines	http://www.microrna.org/microrna/home.do	suite
MicroarrayWorkbench	http://wiki.c2b2.columbia.edu/workbench/index.php/QuickStart	suite
NIA Array Analysis	http://lgsun.grc.nia.nih.gov/ANOVA/index.html	suite
oompa	http://bioinformatics.mdanderson.org/Software/OOMPA/	suite
read Riken Expression Array Database	http://read.gsc.riken.go.jp/	suite
Robin - MapMan	http://mapman.gabipd.org/web/guest/robin	suite
SBEAMS	http://www.sbeams.org/Microarray/	suite
ScoreGenes	http://www.compbio.cs.huji.ac.il/scoregenes/	suite
SeqExpress	http://www.seqexpress.com/	suite
STEM	http://www.cs.cmu.edu/~jernst/stem	suite
SVDMAN	http://public.lanl.gov/mewall/svdman/	suite
Vampire	http://genome.ucsd.edu/microarray/	suite
Vextor Xpression	http://register.informaxinc.com/solutions/xpression/main.html	suite
stem Short Time-series Expression Miner	http://www.cs.cmu.edu/~jernst/stem/	Time series
ChromoViz	http://www.snubi.org/software/ChromoViz/	visualization
ciMiner	http://discover.nci.nih.gov/nature2000/tools/cimmaker.jsp	visualization
F-scan	http://abs.cit.nih.gov/fscan/	visualization
Java Treeview	http://sourceforge.net/projects/jtreeview/	visualization
pca svd	http://public.lanl.gov/mewall/kluwer2002.html	visualization