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MicroArray Software available
- EisenLab ( rana.lbl.gov ) Window
version only. Manuals & Source Codes available. Free for academic use.
- ScanAlyze: overview of functionality
Process fluorescent images of microarrays. Includes semi-automatic definition
of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database.
Manual.
- Cluster: overview of functionality
Performs a variety of clustering and other analysis functions on large microarray datasets.
Currently includes hierarchical clustering, self-organizing maps (SOMs), k-means clustering, and principal
component analysis. Manual.
- TreeView:
Graphically browse results of clustering and other analyses from Cluster.
Supports tree-based and image based browsing of hierarchical trees. Multiple output formats
for generation of images for publications. No manual available.
- Scanalytics ( www.scanalytics.com )
- IPLab with MicroArray Suite Extension:
an image analysis software used specifically for extracting and visualizing DNA microarray data. It consists of a
package of software extensions for Scanalytics' IPLab core program, and is capable of performing a comprehensive
analysis of microarray images generated by virtually any scanning device. Originally at Laboratory of Cancer Genetics
at NHGRI, NIH. Some of tools include: [1] LoadSKN, which loads images from the NIH scanner or other scanning instruments,
[2] AlignArray, which aligns two images in case the images from red and green channels were scanned separately,
[3] DeArray, which is the central processing tool controlling most of image processing tasks, including target segmentation,
background intensity estimation and probe intensity extraction; and [4] TargetLocator, which reports target information,
refines statistics, and performs some image enhancement tasks. The program opens pairs of microarray images, superimposes
and aligns them, grids and measures target spot intensities and subtracts local background, normalizes overall intensity
differences between images, and then calculates accurately the red/green intensity ratio for each target.
- BioDiscovery ( www.biodiscovery.com )
- ImaGene:
Semi-Automated array image analysis. It
measures and visualizes gene expression data from high-density array images.
- GeneSight:
Performs the following kinds
of analysis: automated gene annotation integration, statistical significance testing, replicate data processing, direct
data querying, Affymetrix GeneChip compatibility, statistical confidence analysis, k-means clustering, pattern similarity
searching, time series analysis, gene group intersections and unions, non-linear normalization, hierarchical clustering,
universal data file import, self-organizing maps, and principal component analysis.
- Axon Instruments (www.axon.com ).
- GenePix Pro 3.0:
GenePix Pro software analyzes data from both Axon and non- scanners. Fully scriptable acquisition and
analysis, fast auto-align, integrated with web-based databases for point-and-click database access.
- Imaging Research ( www.imagingresearch.com )
- Cose (www.cose.fr )
- XdotsReader:
Image analysis software with automatic grid detection and statistic, comparison, normalization and
graphical tools.
- Applied Maths ( www.applied-maths.com )
- GenExplore/GenMath:
Performs the following kinds of analysis: clustering, PCA, self-organizing maps (SOM),
pattern matching, and data visualization (scatter-plots etc.). Can run in script mode. Manual.
PDF brochure.
- GeneData ( www.genedata.com )
- GeneData Expressionist:
Extensive data analysis software with k-means clustering, pattern correlations,
hierarchical clustering, self-organizing maps, etc.
PDF brochure.
Other Software Providers:(found at www.gene-chips.com )
- Molecular Pattern Recognition web site at MIT's
Whitehead Genome Center. Focuses on computational
methodologies for the analysis and
interpretation of large-scale expression data sets generated by DNA
micro-array experiments.
- Imaging Research, Inc., St. Catharines, Ontario, Canada.
The company writes software, develops detection technologies, and integrates systems for image analysis. Its
PC-based ArrayVision™
system has been widely used for rapid and automated analysis of genome arrays.
- LION Bioscience AG's
arraySCOUT™is a new software for analyzing gene
expression data. arraySCOUT™ is able to link all expression data to internal
and external biological databases via SRS. This link provides information on
the function, structure and metabolic pathways of genes from up to 400
databases.
- Molecular Applications Group, Palo Alto, CA.
Stingray™ is integrated software and database products for gene
expression, gene function, and gene sequence analysis from microarray data. It is integrated with and dependent upon the
use of Affymetrix's GeneChip® system and its
Expression Data Mining Tool (EDMT) software. [Its ownership of and rights to
Stingray™ were sold to Affymetrix in December, 1999.] No longer a corporate
entity.
- MolecularWare, Inc.: ArrayAnalyzerDB
- Partek, Inc., St. Peters, Missouri. Provider of pattern recognition
and data visualization software for science and engineering. Its Partek Pro 2000
system has been used by companies to analyze microarray gene expression data.
- Rosetta Inpharmatics, Kirkland, Washington.
Resolver™ Expression Data Analysis System.
- SilicoCyte
automated image analysis,
auto-gridding, auto-segmentation, comprehensive gene annotation, statistical
significance testing, replicate data processing, direct data querying,
statistical error models, differential expression, k-means clustering,
profile searching, ANOVA, advanced visualization, hierarchical clustering,
universal data file import, principal component analysis and quality control
reporting for data validation.
Updated February 2004: SilicoCyte v1.3 is now available with additional features such as Self
Organizing Maps (SOM), Venn Analysis, M Vs A Plot.
- Silicon Genetics'
GeneSpring™ workbench for
analyzing experiments based upon genomic expression experiments.
- Spotfire, Inc., Cambridge, Massachusetts. Offers
advanced data visualization capabilities including the ability to perform gene
cluster analysis and metabolic pathway mapping. The Spotfire Array Explorer is
particularly attractive to experimentalists performing microarray analysis.
- Media Cybernetics, L.P., Silver Spring, MD: Array-Pro.
- Microarray Software developed by Stanford University
- Synomics Ltd., Cambridge, UK (bioinformatics)
- TIGR (The Institute for Genome Research) offers software tools
(free for academic institutions) for array analysis.
- Dr. Terry Speed's Microarray Data Analysis Group Page:
very good resource on statistics aspects of microarray data [Berkeley]
- GCG's SeqArray Improves MicroArray Data Analysis,
Visualization, and Management
- PREMIER Biosoft International, Palo Alto, CA.
Array Designer
- designs PCR primers and oligonucleotide probes for microarrays
- OmniViz, Inc., Columbus, OH, a subsidiary of
Battelle. Provides information visualization and data mining solutions for life and chemical sciences. Product:
OmniViz Pro
- ViaLogy Corp., utilizes quantum interferometric
computing to analyze biochips
- Xpogen Inc., Cambridge, MA. Web-based tools for organizing, sharing, analyzing,
and interpreting gene expression microarray data and associated annotation.
"
relevance networks".
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