Microarray Software List

[moleculardude]

Free Software for DNA and Protein Microarrays:

AFM (Array File Maker) - Samuel Lunenfeld Research Institute, Mount Sinai Hospital (Toronto)
[Only registered users see links. ]

AMADA (Analyzing Microarray Data) - Univ of Hong Kong
[Only registered users see links. ]

ANOVA programs for microarray data - Churchill's group at Jackson Lab
[Only registered users see links. ]

ANOVARRAY - SAS macros
[Only registered users see links. ]

BABELOMICS - Centro de Investigacion Principe Felipe, Spain
[Only registered users see links. ]

CHIPINFO (retrieving annotation information from NetAffx and Gene Ontology): - Wong's lab at Harvard Univ
[Only registered users see links. ]

CLUSFAVOR (CLUSter and Factor Analysis using Varimax Orthogonal Rotation), - Baylor
[Only registered users see links. ]

CLUSTER, TREEVIEW: - Eisen's lab at Lawrence Berkeley National Lab
[Only registered users see links. ]
also, [Only registered users see links. ]

CYBER-T - web interface for t-test, regularized t-test, etc.
[Only registered users see links. ]

CYTOSCAPE : visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
[Only registered users see links. ]

D-CHIP: specifically for Affymetrix chip data - Wong lab at Biostatistics Department, Harvard University
[Only registered users see links. ]

DNC-MIX: models the distribution of the gene expression profile as a mixture, - Lin group at Ohio State University
[Only registered users see links. ]

GENE@WORK : IBM Research
[Only registered users see links. ]

GENE-CLUSTER: Whitehead Institute (registration is required). Commercial version at Affymetrix
[Only registered users see links. ]

GENE-PATTERN : Broad Institute.
[Only registered users see links. ]

GEDA: gene expression data analysis. Univ Pittsburg
[Only registered users see links. ]

GEDS: gene expression data simulator - University of Pittsburg
[Only registered users see links. ]

GEPAS : gene expression pattern analysis suite - Centro de Investigacion Principe Felipe, Spain
[Only registered users see links. ]

GOSURFER - Wong lab at Harvard University
[Only registered users see links. ]

J-EXPRESS - University of Bergen, Norway
[Only registered users see links. ]

MAANOVA - Jackson Lab,
[Only registered users see links. ]

ONTO-EXPRESS - Wayne Univ
[Only registered users see links. ]

PAGE (PAtterns from Gene Expression) - Univ. Penn.
[Only registered users see links. ]

PLAID - Owen lab at Stanford Univ.
[Only registered users see links. ]

R_SVM (recursive sample classification by SVM) - Wong lab at Harvard Univ
[Only registered users see links. ]

SAM (significance analysis of microarrays) - Tibshirani's group at Stanford Univ.
[Only registered users see links. ]

SAM (significance of array measurement) - Institute for Systems Biology
[Only registered users see links. ]

SMA (Statistic for Microarray Analysis, in R or S-PLUS subroutines) - Speed's lab at Statistics Department of UC Berkeley
[Only registered users see links. ]

STEM (short time-series expression miner): from Carnegie Mellon Univ
[Only registered users see links. ]

SVDMAN: from Los Alamos National Laboratory
[Only registered users see links. ]

TREE-ARRANGE and TREEPS : from Univ Waterloo
[Only registered users see links. ]

VERA (variability and error assessment) - Institute for Systems Biology
[Only registered users see links. ]

XCLUSTER - Sherlock's lab of Genetics Department of Stanford Univ
[Only registered users see links. ]

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.