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Microarray Data Analysis
Statistical Analysis Software
Institutions or companies which produce data analysis software
for cDNA microarray slides.
- BASE (BioArray Software Environment). Microarray database server
with normalization and some analysis facilities. Lund University, Sweden.
- Bengtsson, Henrik. Develops aroma, an elegant R package for microarray normalization, diagnostics and data analysis using a custom
object-orientated system.
- Bioconductor. An R-based
development project for open-source genomic software. Includes a
number of important packages. Coordinated by
Robert Gentleman, Fred Hutchinson Cancer Center.
- BioSieve. Produce ExpressionSieve,
a microarray data analysis, data mining and data visualization software
package written in Java.
- Broad Institute of MIT and Harvard.
Produce the GenePattern
package for genomics and microarray analysis.
- Eisen Lab. Distribute ScanAlyze,
Cluster
and TreeView free for non-profit researchers.
- Biodiscovery. GeneSight.
- Genedata. Produce Expressionist
software for large scale gene expression analysis.
- GeneSifter.Net. A web-based
data analysis tool for Affymetrix microarrays created by VizX Labs, Seattle.
- Gerstein Lab (Yale University).
ExpressYourself is an
online platform for pre-preprocessing of microarray data.
- InforMax (Array Pro, Vector
Xpression).
- Iobian Informatics. GeneTraffic
is
microarray database and data analysis software based on open software.
- Molecular Devices. Acuity for data warehousing,
analysis and visualization.
- Molmine (J-Express). Java software.
- National Center for Genome Resources (GeneX).
- PAM: Prediction Analysis
for Microarrays. Robert Tibshirani, Stanford University.
- Pevsner Lab, (Kennedy Kreiger Institute).
SNOMAD (Standardization and NOrmalization of MicroArray Data).
- Partek. Produce Partek Pro software
for statistical analysis and visualisation including gene expression.
- PermutMatrix. MS
Windows software for clustering and seriation analysis of gene expression
data. Gilles Caraux, LIRMM, France.
-
Churchhill Lab (Jackson Laboratories). maanova for analysis of variance with microarray data.
- Rosetta Inpharmatics. No links to
software on their www pages.
- Silicon Genetics. Genespring
is a very popular program for general data analysis of microarray data.
- SilicoCyte. Integrated commercial
analysis solution.
- Spotfire. DecisionSite software for
functional analysis.
- Speed Group
(University of California, Berkeley).
R package sma (Statistical Microarray
Analysis), Windows application RMAExpress and contributions to the
Bioconductor project.
- TIGR. SpotFinder image
analysis, MIDAS data management, MeV differential expression analysis.
- Probability of Expression (POE).
An approach to the analysis of gene expression microarrays using
three-component mixtures. Giovanni Parmigiani, Johns Hopkins.
- SuperArray.
- Townsend Lab, University of Connecticut.
Produces BAGEL (Bayesian Analysis of Gene Expression Levels) for the
statistical analysis of spotted microarray data, Pathway Processor to test for overrepresentation of
differentially expressed genes within known pathways of S. cerevisiae or B.
subtilis, and SeqPop for computing population genetics statistics on
sequence data.
- University of
Pittsburgh & UPMC Bioinformatics Web-Tools Collection. Includes expression
analysis tool with www interface.
- Walter and Eliza Hall Institute of
Medical Research. Produce R package limma (linear models and differential expression
for microarray data) and associated user-interfaces limmaGUI and
affylmGUI.
- Wong Lab (Harvard
University). DNA-Chip Analyzer.
- Yang, Jean (University of Sydney). R packages marray,
DEDS and stepNorm.
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