Microarray Software List

[moleculardude]

Free Software for DNA and Protein Microarrays:

AFM (Array File Maker) - Samuel Lunenfeld Research Institute, Mount Sinai Hospital (Toronto)
Software

AMADA (Analyzing Microarray Data) - Univ of Hong Kong
http://web.hku.hk/~xxia/software/AMADA.htm

ANOVA programs for microarray data - Churchill's group at Jackson Lab
http://www.jax.org/research/churchil...ova/index.html

ANOVARRAY - SAS macros
AnovArray — MIG

BABELOMICS - Centro de Investigacion Principe Felipe, Spain
www.babelomics.org

CHIPINFO (retrieving annotation information from NetAffx and Gene Ontology): - Wong's lab at Harvard Univ
ChipInfo

CLUSFAVOR (CLUSter and Factor Analysis using Varimax Orthogonal Rotation), - Baylor
http://mbcr.bcm.tmc.edu/genepi/

CLUSTER, TREEVIEW: - Eisen's lab at Lawrence Berkeley National Lab
EisenLab
also, http://www.microarrays.org/software.html

CYBER-T - web interface for t-test, regularized t-test, etc.
Welcome to Cyber-T

CYTOSCAPE : visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
Cytoscape: Analyzing and Visualizing Network Data

D-CHIP: specifically for Affymetrix chip data - Wong lab at Biostatistics Department, Harvard University
dChip

DNC-MIX: models the distribution of the gene expression profile as a mixture, - Lin group at Ohio State University
DNC_MIX

GENE@WORK : IBM Research
IBM Research | Projects | Functional Genomics and Systems Biology - Automatic Redirection

GENE-CLUSTER: Whitehead Institute (registration is required). Commercial version at Affymetrix
http://www.genome.wi.mit.edu/MPR/software.html

GENE-PATTERN : Broad Institute.
GenePattern

GEDA: gene expression data analysis. Univ Pittsburg
caGEDA: A web application for the integrated analysis of global gene expression patterns in cancer

GEDS: gene expression data simulator - University of Pittsburg
http://www.contentsoft.de/index.htm?geneviz.htm

GEPAS : gene expression pattern analysis suite - Centro de Investigacion Principe Felipe, Spain
www.gepas.org

GOSURFER - Wong lab at Harvard University
GoSurfer

J-EXPRESS - University of Bergen, Norway
J-Express

MAANOVA - Jackson Lab,
MAANOVA 2.0 - The Jackson Laboratory

ONTO-EXPRESS - Wayne Univ
Intelligent Systems and Bioinformatics Laboratory

PAGE (PAtterns from Gene Expression) - Univ. Penn.
PaGE - Patters from Gene Expression

PLAID - Owen lab at Stanford Univ.
Plaid models for dna microarray data

R_SVM (recursive sample classification by SVM) - Wong lab at Harvard Univ
http://biosun1.harvard.edu/~xzhang/R-SVM/R-SVM.html

SAM (significance analysis of microarrays) - Tibshirani's group at Stanford Univ.
Significance Analysis of Microarrays

SAM (significance of array measurement) - Institute for Systems Biology
Institute for Systems Biology: Home

SMA (Statistic for Microarray Analysis, in R or S-PLUS subroutines) - Speed's lab at Statistics Department of UC Berkeley
R package: Statistics for Microarray Analysis (SMA)

STEM (short time-series expression miner): from Carnegie Mellon Univ
STEM: Short Time-series Expression Miner

SVDMAN: from Los Alamos National Laboratory
http://public.lanl.gov/mewall/svdman/

TREE-ARRANGE and TREEPS : from Univ Waterloo
Bioinformatics Research at the University of Waterloo

VERA (variability and error assessment) - Institute for Systems Biology
Institute for Systems Biology: Home

XCLUSTER - Sherlock's lab of Genetics Department of Stanford Univ
Clustering Program

Please post your reviews of this microarray software below.

Cheers!
Moleculardude

[yeaster]

The software list is impressive.
I only used SAM. If you want to analyse replicates of the same experiment SAM can do the job. You can get genes that are significantly up or downregulated across your replicates. You will also get the average fold changes for significant genes. The problem I had with SAM is that I had groups of replicates with common control. I wanted the fold difference between groups of replicates, not within the group. Sam could not do this. I used ANOVA for this but it gives you significantly different genes between groups, without fold changes. I am still struggling with this.
I also used mev4 (TIGR) software. It is very good for freeware.

[yeaster]

The software list is impressive.
I only used SAM from this list. If you want to analyse replicates of the same experiment SAM can do the job. You can get genes that are significantly up or downregulated across your replicates. You will also get the average fold changes for significant genes. The problem I had with SAM is that I had groups of replicates with common control. I wanted the fold difference between groups of replicates, not within the group. Sam could not do this. I used ANOVA for this but it gives you significantly different genes between groups, without fold changes. I am still struggling with this.
I also used mev4 (TIGR) software. It is very good for freeware. My favorit is still Genespring. What you pay is what you get.