| Microarray Resources : Software & Tools | ||
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| The tables below are not intended to be a comprehensive list. A more detailed resource for software comparison, compiled by Y.F. Leung, can be found here. | ||
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| Stanford Software | |||
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| Program | Description | Author | Platform |
| CaryoScope | Viewing aCGH or expression data in a whole-genome context. | Ihab Awad | Java |
| CGH-Miner | Calling Gains and losses in Array CGH data using the CLAC Method. | Wang et al. | Excel Add-in/ R package |
| Cluster | Perform hierarchical clustering, self-organizing maps | Michael Eisen | Windows |
| GeneXplorer | Web-visualization of microarray datasets | Rees/Demeter/Matese | Perl |
| GO-TermFinder | Finds GO terms significantly associated with a list of genes | Gavin Sherlock | Perl |
| HeatMap Builder | Generates customizable heatmaps from microarray data | Euan Ashley, Josh Spin, Clifton Watt | Windows |
| Java Treeview | View Results of Clustering | Alok Saldhana | Java |
| KNNimpute | Estimation of missing microarray values | Olga Troyanskaya |
UNIX Linux |
| PAM | Prediction Analysis for Microarrays | Hastie/Naras/Tibshirani | Excel /R under Windows/Unix |
| SAM | Significance Analysis of Microarrays : Supervised learning software for genomic expression data mining | Rob Tibshirani | Excel Add-in |
| ScanAlyze | Processes fluorescent images of microarrays | Michael Eisen | Windows |
| SLCView | Creates images in many different formats from cdt and gtr files, from the unix command-line | Swaine Lin Chen | UNIX/Linux |
| SMD Package | Full source code for the Stanford Microarray Database | SMD Staff | UNIX + Oracle |
| SuperPC | Survival and regression analysis for microarrays | Bair/Tibshirani | R package |
| TreeView | Graphically browse results of clustering and other analyses from Cluster | Michael Eisen | Windows |
| XCluster | Perform hierarchical clustering, self-organizing maps | Gavin Sherlock |
UNIX Linux MacOS Windows |
| Software from other sources | |||
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| Program | Description | Provider | Platform |
| Array Designer | Tool assisting in primer design for microarray construction | Premier Biosoft International | JAVA |
| ArrayMiner® | Set of analysis tools using advanced algorithms to reveal the true structure of gene expression data. | Optimal Design, Sprl. |
Windows MacOS |
| ArrayViewer | Identification of statistically significant hybridization signals | National Human Genome Research Institute | JAVA |
| ArrayVision | Automated analysis of macro & microarrays | Imaging Research Inc. | Windows |
| BAGEL | Bayesian Analysis of Gene Expression Levels: a program for the statistical analysis of spotted microarray data. | University of Connecticut | MacOS, Windows, Linux |
| BAMarray | Bayesian Analysis of Variance for Microarrays - detect differentially expressed genes from multigroup microarray data | Case University | Windows, Linux |
| BASE | Microarray database and analysis platform | Lund University | Web |
| Cluster 3.0 | An enhanced version of Mike Eisen's Cluster | University of Tokyo, Japan |
UNIX Linux MacOS Windows |
| DNA arrays analysis tools | Hierarchical clustering, Self Organizing Maps and more | Spanish National Cancer Center, Bioinformatics Unit | Web |
| Expression Profiler | Analysis & clustering of gene expression data | European Bioinformatics Institute (EBI) | Web |
| ExpressionSieve | Microarray data analysis package, strong in linking biological significance to expression patterns, data and analysis process management, signature gene discovery and class discovery & prediction. | BioSieve | Java |
| GEDA | Gene expression data analysis and simulation tools, offering a variety of options for processing and analyzing results. | University of Pittsburgh and UPMC | Web |
| GeneCluster | Self-organizing maps | Whitehead Institute/MIT Center for Genome Research |
JAVA Windows NT |
| GenMAPP | Tools for visualizing data from gene expression experiments in the context of biological pathways. | Conklin lab; Gladstone Institute & the UCSF | Windows |
| GeneSifter | The GeneSifter microarray data analysis system provides access to powerful statistical tools through a web interface, with integrated features for determining the biological significance of the data. GeneSifter works with any array format and is especially optimized for Affymetrix GeneChip users. Free trial accounts available. | GeneSifter | Web |
| GeneX | Gene Expression Database : integrated toolset for data analysis and comparison | National Center for Genome Resources |
Windows Linux SunOS/Solaris |
| GenMaths | Analysis of high density microarrays and gene chips | Applied Maths | Windows |
| Genowiz™ | A Gene Expression Data Analysis and Management Tool. | Ocimum Biosolutions |
Windows Macintosh Unix Linux Solaris |
| MicroArray Suite | Extracting and visualizing DNA microarray data | Scanalytics Inc. | MacOS |
| Partek Pattern Recognition | Extracting and visualizing patterns in large multivariate data | Partek Incorporated | Linux, Unix, Windows |
| TIGR MultiExperiment Viewer | Analysis and Visualization of Microarray Data | TIGR | JAVA |
| TreeArrange and Treeps | Software for displaying and manipulating hierarchical clustered data | University of Waterloo, Canada |
Linux Unix Windows |
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Hardware |
Please send comments or questions to: array@genome.stanford.edu |