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Image Analysis | Pre-processing and Statistics Software | Data Mining | Database Software

Microarray Publications:

Published using OMCF or BIOinfOSU

Published on PubMed within the last 30 days

Published on PubMed within the last 90 days

Published on PubMed within the last 180 days

Published on PubMed within the last year

Published on PubMed before 1999 or within 1999, 2000, 2001, 2002, 2003, 2004

Published on PubMed to date

Helpful sites/information listed in no particular order:

Microarray troubleshooting: image gallery
Microarray troubleshooting guide from Genisphere
Technical Aspects of Microarray Production
A Concise Guide to cDNA Microarray Analysis – II
The-Science-Lab.com - directory of Biology related websites

Software for microarray analysis and databases:

I. Image Analysis Software

a. Free for academic users

Dapple from Washington University in St. Louis. (UNIX/Linux/Mac OSX)
F-scan from NIH (UNIX/Linux, Windows, Mac)
ScanAlyze from Michael Eisen's lab (Windows)
Spotfinder from TIGR (Windows)
UCSF Spot from Jain Lab at UCSF (Windows)

b. Commercial

GenePix Pro from Axon Instruments (Windows)
ImaGene from BioDiscovery (Windows)
ArrayPro from MediaCybernetics (Windows)
ArrayVision from Imaging Research, Inc (Windows)

II. Pre-processing and Statistics Software

a. Free for academic users

GPAP from OSU Microarray Core and Bioinformatics Resource Facilities (Web)
Bioconductor and R-project statistical environment
ANOVA from Churchill Group at The Jackson Laboratory (Linux, Windows)
BRB ArrayTools (MS Excel add-in) from National Cancer Institute (Windows)
SAM MS Excel add-on from Stanford (Windows)
SNOMAD from Pevsner Lab at Johns Hopkins School of Medicine (WEB)
VERA and SAM from the Institute for Systems Biology (Unix/Linux, Windows)

b. Commercial

ArrayStat from Imaging Research, Inc (Windows)
GeneSpring from Silicon Genetics (Linux, Windows, Mac)
Acuity from Axon Instruments (Windows)
SpotFire from SpotFire (Windows)
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III. Data mining/visualization software

a. Free for academic users

MeV: MultiExperiment Viewer from TIGR (Windows)
Genesis from Graz University of Technology (Windows)
CLUSFAVOR from Baylor College of Medicine (Windows)
Cluster and Treeview from Michael Eisen's Lab (Windows)
DNA-arrays analysis tools (various tools) from Spanish National Cancer Center (WEB)
Expression Profiler (various tools) from EBI (WEB)
GeneCluster from Broad Institute (UNIX, Windows)
MAExplorer from NCI LEBC (UNIX/Linux, Windows, Mac, Mac OSX)
XCluster from Stanford (Unix/Linux, Windows, Mac)

b. Commercial

GeneSpring from Silicon Genetics (Linux, Windows, Mac)
Acuity from Axon Instruments (Windows)
SpotFire from SpotFire (Windows)
Genowiz from Ocimunbio
J-Express from MolMine (Windows)
arraySCOUT from Lion Biosciences (UNIX, Windows)
GeneSight from BioDiscovery (Windows)
PathwayAssist from Stratagene
Rosetta Resolver System from Rosetta Biosoftware (Unix)
Xpression from Invitrogen (Windows)

IV. Database Software and Services

a. Free for academic users (or all)

GEO at NCBI
AMAD flatfile database from UCSF (Unix/Linux, Windows, Mac web servers)
ArrayDB from NHGRI ((Unix/Linux web server)
BASE from Lund University (Linux/MySQL)
Longhorn (LAD) from UT Austin
GeneX-Lite and GeneX Server from NCGR
MADAM: MicroArray DAta Manager from TIGR
maxd from Manchester Bioinformatics (Unix/Linux)
NOMAD from UCSF (Unix/Linux, Mac OSX)

b. Commercial