public domain ("free") programs for microarray data analysis

	Bibliography on Microarray Data Analysis	front\| books \| preprints \| 2009 \| 2008 \| 2007 \| 2006 \| 2005 \| 2004 \| 2003 \| 2002 \| 2001 \| 2000 \| 1999 \| 1998 \| 1997 \| 1996 \| 1995 \| 1994 \| 1993 \| core facilities\| data\| mailing \| programs(free) \| analysis groups \| labs \| companies \| short-courses\| lists \| mirror © Copyright, 1999-2009 Wentian Li of North Shore LIJ Research Institute
http://www.nslij-genetics.org/microarray/

see also, YukFai Leung's microarray analysis and database softwares comparison page
Korbinian Strimmer's R packages for gene expression analysis

public domain programs

AFM (Array File Maker): from Samuel Lunenfeld Research Institute, Mount Sinai Hospital (Toronto)
http://www.mshri.on.ca/tyers/software.html
AMADA (Analyzing Microarray Data): from Univ of Hong Kong
http://web.hku.hk/~xxia/software/AMADA.htm
ANOVA programs for microarray data: from Churchill's group at Jackson Lab
http://www.jax.org/research/churchill/software/anova/index.html
ANOVARRAY : SAS macros
http://www-mig.jouy.inra.fr/stat/AnovArray
BABELOMICS , from Centro de Investigacion Principe Felipe, Spain
http://www.babelomics.org/
CHIPINFO (retrieving annotation information from NetAffx and Gene Ontology): from Wong's lab at Harvard Univ
http://biosun1.harvard.edu/complab/chipinfo/
CLUSFAVOR (CLUSter and Factor Analysis using Varimax Orthogonal Rotation), from Baylor
http://mbcr.bcm.tmc.edu/genepi/
CLUSTER, TREEVIEW: from Eisen's lab at Lawrence Berkeley National Lab
http://rana.lbl.gov/EisenSoftware.htm
also, http://www.microarrays.org/software.html
CYBER-T : web interface for t-test, regularized t-test, etc.
http://visitor.ics.uci.edu/genex/cybert/
CYTOSCAPE : visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
http://www.cytoscape.org/
D-CHIP: specifically for Affymetrix chip data, from Wong's lab at Biostatistics Department, Harvard University
http://www.dchip.org
DNC-MIX: models the distribution of the gene expression profile as a mixture, from Lin's group at Ohio State University
http://www.stat.ohio-state.edu/~statgen/SOFTWARE/DNC-MIX/
GENE@WORK : IBM Research
http://www.research.ibm.com/FunGen/NewFiles/FGDownloads.htm
GENE-CLUSTER: Whitehead Institute (registration is required). A commercial version of this program is also developed, at Affymetrix
http://www.genome.wi.mit.edu/MPR/software.html
GENE-PATTERN : Broad Institute.
http://www.broad.mit.edu/cancer/software/genepattern/
GEDA: gene expression data analysis. Univ Pittsburg
http://bioinformatics.upmc.edu/GE2/GEDA.html
GEDS: gene expression data simulator. Univ Pittsburg
http://www.contentsoft.de/index.htm?geneviz.htm
GEPAS : gene expression pattern analysis suite. from Centro de Investigacion Principe Felipe, Spain
http://www.gepas.org/
GOSURFER : Wong's lab at Harvard Univ
http://biosun1.harvard.edu/complab/gosurfer/
J-EXPRESS: Univ of Bergen, Norway
http://www.ii.uib.no/~bjarted/jexpress/index.html
MAANOVA : Jaclson Lab,
http://www.jax.org/staff/churchill/labsite/software/anova/index.html
ONTO-EXPRESS : Wayne Univ
http://vortex.cs.wayne.edu/Projects.html
PAGE (PAtterns from Gene Expression): from U Penn.
http://www.cbil.upenn.edu/PaGE/
PLAID : from Owen's lab at Stanford Univ.
http://www-stat.stanford.edu/~owen/plaid/
R_SVM (recursive sample classification by SVM): from Wong's lab at Harvard Univ
http://biosun1.harvard.edu/~xzhang/R-SVM/R-SVM.html
SAM (significance analysis of microarrays): from Tibshirani's group at Stanford Univ.
http://www-stat.stanford.edu/~tibs/SAM/index.html
SAM (significance of array measurement): from Institute for Systems Biology
http://www.systemsbiology.org/VERAandSAM/
SMA (Statistic for Microarray Analysis, in R or S-PLUS subroutines): from Speed's lab at Statistics Department of UC Berkeley
http://www.stat.berkeley.edu/users/terry/zarray/Software/smacode.html
STEM (short time-series expression miner): from Carnegie Mellon Univ
http://www-2.cs.cmu.edu/~jernst/stem/
SVDMAN: from Los Alamos National Laboratory
http://public.lanl.gov/mewall/svdman/
TREE-ARRANGE and TREEPS : from Univ Waterloo
http://monod.uwaterloo.ca/downloads/treearrange/
VERA (variability and error assessment): from Institute for Systems Biology
http://www.systemsbiology.org/VERAandSAM/
XCLUSTER: from Sherlock's lab of Genetics Department of Stanford Univ
http://genome-www.stanford.edu/~sherlock/cluster.html

public domain programs - image processing

ArrayTools : from Biometric research branch, NCI/NIH
http://linus.nci.nih.gov/BRB-ArrayTools.html
ARRAY-VIEWER: from TIGR (The Institute for Genomic Research)
http://www.tigr.org/softlab/
DAPPLE : from Washington Univ at St. Louis
http://www.cs.wustl.edu/~jbuhler/research/dapple/
F-SCAN (Fluorescently Probed cDNA Microarray Analysis): from Center for Information Technology, NIH
http://abs.cit.nih.gov/fscan/
P-SCAN (Peak quantification using Statistical Comparative ANalysis): from Center for Information Technology, NIH
http://abs.cit.nih.gov/pscan/
SCAN-ALYZE: from Eisen's lab at Lawrence Berkeley National Lab
http://rana.lbl.gov/EisenSoftware.htm
also, http://www.microarrays.org/software.html

public domain programs - data management

GENEX : from National Center for Genome Resources
http://www.ncgr.org/genex/index.html
MAPS (MicroArray Project System): from National Institute of Environmental Health Sciences (NIH)
http://dir.niehs.nih.gov/microarray/software/maps/