Freely available software for analyzing Affymetrix data

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Freely available software for analyzing Affymetrix data

BioConductor - R Package http://www.bioconductor.org/
R package for Microarray analysis contains (and can be downloaded individually)
- Biobase - Base functions for Bioconductor
- annotate - Annotation for microarrays
- affy - Methods for Affymetrix Oligonucleotide Arrays
- AnnBuilder - Bioconductor annotation data builder
- edd - expression density diagnostics
- genefilter - Genefilter: filter genes
- geneplotter - Geneplotter: plot microarray data
- rhdf5 - An HDF5 interface for R
- marrayNorm - Location and scale normalization for cDNA microarray data
- marrayClasses - Classes and methods for cDNA microarray data
- marrayInput - Data input for cDNA microarrays
- marrayPlots - Diagnostic plots for cDNA microarray data
- multtest - Multiple Testing Procedures
- ROC - utilities for ROC, with microarray focus
- tkWidgets - R based tk widgets

European Bioinformatics Institute (EMBL-EBI) http://www.ebi.ac.uk/microarray/
Software - Expression Profiler

Gary Churchill's Statistical Genetics Group - http://aretha.jax.org/jax-cgi/churchill/index.cgi
Software Includes R/maanova 0.8-1 and MA-ANOVA 1.2

Gladstone Institute, UCSF http://www.gladstone.ucsf.edu/
Software - GenMAPP

Lund University, Theoretical Physics
Software - BASE (BioArray Software Environment)

NCGR (National Center for Genomic Research) http://www.ncgr.org/
Software:
- GeneX
- PathDB
- ISYS
- XGI

Speed Lab http://www.stat.berkeley.edu/users/terry/zarray/Html/index.html
R package - Statistics for Microarray Analysis

Stanford Microarray Database http://genome-www5.stanford.edu/MicroArray/SMD/index.shtml
Software:

Statistical Genetics, Rockefeller University
Meta index - a collection of papers with an emphasis on microarray data

TIGR http://www.tigr.org/
Software
TIGR MultiExperiment Viewer (MEV v2.1)

Broad Institute Cancer Program http://www.broad.mit.edu/cancer/
Software - GeneCluster 2.1b and GeneCluster 1.0

Wong Lab http://www.biostat.harvard.edu/complab/
Software:

The Bioinformatics Group at the Graz University of Technology http://genome.tugraz.at/
Software - Genesis

Genevestigator, a set of web tools to help analyze Affymetrix mouse and Arabidopsis gene expression chips.

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