Resource Center > Free Academic Microarray Resources

Image Quantification Software

Data Analysis Software

Functional Analysis Software

Links to Academic Core Facilities



[ image quantification software ]

ScanalyzeStanford software used for processing fuorescent microarray images. Includes semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database.
SpotfinderTIGR image quantification software that reads tiff images and allows for removal of saturated spots. Data outputs to tab-delimited files that can be exported to excel.
F-ScanNIH software for quantifying fluorescent images. F-Scan requires MATLAB software and a UNIX account. Analyses include scatterplots, multiple image comparison, data merging.
P-ScanNIH software for quantifying peak intensities from images generated from membranes scanned using a phosphoimager. P-Scan requires MATLAB software access and a UNIX account.
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[ data analysis software ]

CAGEDCAGED (Cluster Analysis of Gene Expression Dynamics) is a computer program for the analysis of temporal gene expression data. CAGED is based on a method called Bayesian Clustering by Dynamics, which identifies the most probable set of clusters given a set of time series (it can be used as a Bayesian clustering program on a-temporal expression data).
dChipDNA-Chip Analyzer (dChip) is a software package implementing model-based expression analysis of oligonucleotide arrays and several high-level analysis procedures (particularly useful for Affymetrix arrays). High-level analysis in dChip includes comparative analysis, hierarchical clustering, SNP analysis etc. (Li and Wong, 2001 [Pubmed])
SAM: Significance Analysis of MicroarraysAn excel add-in that supports supervised learning for genomic expression data mining (uses data permutations to provide estimate of False Discovery Rate for multiple testing).
ClusterClassic cluster analysis software from Eisen lab at Stanford. Currently includes hierarchical clustering, self-organizing maps (SOMs), k-means clustering, principal component analysis.Hierarchical clustering methods described in Eisen et al. (1998) PNAS 95:14863.
TreeViewAllows Graphical visualization for Cluster outputs. Supports tree-based and image based browsing of hierarchical trees.
Cyber-TCyber-T is a a microarray analysis web interface from UCI's Institute for Genomics and Bioinformatics. It accommodates both paired (2-dye) data and data in which control and experiment are on separate experiments (e.g. affymetrix based data). It also supports Bayesian statistical approaches and Bonferroni corrections for significance analysis of differentially expressed clones. GeneX database and analysis tools are written in R and can also be installed locally.
CleaverStanford web accessible microarray data visualization, classification, and clustering software suite. Fast site with userfriendly forms for uploading data to the server site for computations.
SNOMADA collection of algorithms written in R statistical language, directed at the normalization and standardization of DNA microarray data. Useful mostly for paired microarray data.
TM4 (TIGR)A package of open source software programs for microarray analysis from The Institute for Genomic Research. The suite includes MIDAS (Microarray Data Analysis System), MADAM (MicroArray DAta Manager), MEV (MultiExperiment Viewer) and the image processing tool Spotfinder.
BRB Array ToolsIntegrated microsoft excel add-in useful for visualization and statistical analysis of DNA microarray data. Genes can also be annotated by linking to NCBI databases using clone identifiers.
GenePatternGenePattern is a software package from the Broad Institute for the analysis of molecular profiles, e.g., genome-wide microarray expression signatures. It includes a collection of analytic and visualization tools, interfaces for the easy construction of analytic pipelines and integration of new modules without additional programming
Expression ProfilerA collection of EBI web accessible microarray data analysis tools including clustering and gene ontology tools.
IMAGEneA software package for clustering IMAGE clones/ESTs to known genes, and to each other. It is a useful tool to aid in the re-array of IMAGE clones for public distribution.
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[ functional analysis software ]

Onto-ExpressOnto-Express systematically translates genetic fingerprints into functional profiles. Using strings of accession or cluster identification numbers, Onto-Express searches the public databases and returns tables that correlate expression profiles with the cytogenetic gene locations, the biochemical and molecular functions, the biological processes, cellular components and cellular roles of the translated proteins.
DAVID and EASE (NIH) DAVID (Database for Annotation, Visualization and Integrated Discovery) and EASE (the Expression Analysis Systematic Explorer)provide integrated solutions for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteomic platforms.
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[ selected links to academic core facilities ]

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Events
Mar 22-24 2006, Genomes to Systems; Manchester, UK. The latest post-genome developments. [conference web site]
Jun 8-9 2006, CAMDA 2006; North Carolina. The sixth international conference for the Critical Assessment of Microarray Data Analysis. [conference web site]

Microarray links
Microarray Gene Expression Data (MGED) Society
Minimum information about a microarray experiment - MIAME
CAMDA: Critical Assessment of Microarray Data Analysis
EBI Microarray Page
Stanford Microarray Database
The Brown Lab at Stanford
NIH Microarray Project page
NCI Microarray Center
Lab-on-a-chip.com
BioChipNet
Microarray page maintained by Y. F. Leung of Chinese University of Hong Kong
The I.M.A.G.E. consortium