Difference between revisions of "Dataanalysis"
From Genome Technology Core (GTC) wiki - Sequencing and Microarray
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| + | |+ MIT Software | ||
| + | ! Program !! Description !! Platform | ||
| + | |- | ||
| + | ! GSEA | ||
| + | | Determines if a given set of genes shows differences between two biological states || JAVA | ||
| + | |- | ||
| + | ! GeneCluster | ||
| + | |Self-organizing maps | ||
| + | |JAVA, Windows NT | ||
| + | |- | ||
| + | ! Connectivity Map | ||
| + | | Uses pattern-matching algorithms to enable discovery of functional connections between drugs, genes, and diseases | ||
| + | |Web | ||
| + | |- | ||
| + | ! GeneCruiser | ||
| + | | Annotation tool for Affymetrix probes | ||
| + | |Web | ||
| + | |} | ||
{| border="1" | {| border="1" | ||
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|National Human Genome Research Institute | |National Human Genome Research Institute | ||
|JAVA | |JAVA | ||
| + | |- | ||
! BAGEL | ! BAGEL | ||
|Bayesian Analysis of Gene Expression Levels: a program for the statistical analysis of spotted microarray data. | |Bayesian Analysis of Gene Expression Levels: a program for the statistical analysis of spotted microarray data. | ||
|University of Connecticut | |University of Connecticut | ||
|MacOS, Windows, Linux | |MacOS, Windows, Linux | ||
| + | |- | ||
! BAMarray | ! BAMarray | ||
|Bayesian Analysis of Variance for Microarrays - detect differentially expressed genes from multigroup microarray data | |Bayesian Analysis of Variance for Microarrays - detect differentially expressed genes from multigroup microarray data | ||
|Case University | |Case University | ||
|Windows, Linux | |Windows, Linux | ||
| + | |- | ||
! BASE | ! BASE | ||
|Microarray database and analysis platform | |Microarray database and analysis platform | ||
|Lund University | |Lund University | ||
|Web | |Web | ||
| + | |- | ||
! Cluster 3.0 | ! Cluster 3.0 | ||
|An enhanced version of Mike Eisen's Cluster | |An enhanced version of Mike Eisen's Cluster | ||
|University of Tokyo, Japan | |University of Tokyo, Japan | ||
|UNIX, Linux, MacOS, Windows | |UNIX, Linux, MacOS, Windows | ||
| + | |- | ||
! DNA arrays analysis tools | ! DNA arrays analysis tools | ||
|Hierarchical clustering, Self Organizing Maps and more | |Hierarchical clustering, Self Organizing Maps and more | ||
|Spanish National Cancer Center, Bioinformatics Unit | |Spanish National Cancer Center, Bioinformatics Unit | ||
|Web | |Web | ||
| + | |- | ||
! Expression Profiler | ! Expression Profiler | ||
|Analysis & clustering of gene expression data | |Analysis & clustering of gene expression data | ||
|European Bioinformatics Institute (EBI) | |European Bioinformatics Institute (EBI) | ||
|Web | |Web | ||
| + | |- | ||
!GEDA | !GEDA | ||
|Gene expression data analysis and simulation tools, offering a variety of options for processing and analyzing results. | |Gene expression data analysis and simulation tools, offering a variety of options for processing and analyzing results. | ||
|University of Pittsburgh and UPMC | |University of Pittsburgh and UPMC | ||
|Web | |Web | ||
| + | |- | ||
! GenMAPP | ! GenMAPP | ||
|Tools for visualizing data from gene expression experiments in the context of biological pathways. | |Tools for visualizing data from gene expression experiments in the context of biological pathways. | ||
|Conklin lab; Gladstone Institute & the UCSF | |Conklin lab; Gladstone Institute & the UCSF | ||
|Windows | |Windows | ||
| + | |- | ||
!GeneX | !GeneX | ||
|Gene Expression Database : integrated toolset for data analysis and comparison | |Gene Expression Database : integrated toolset for data analysis and comparison | ||
|National Center for Genome Resources | |National Center for Genome Resources | ||
|Windows, Linux, SunOS/Solaris | |Windows, Linux, SunOS/Solaris | ||
| + | |- | ||
! TIGR MultiExperiment Viewer | ! TIGR MultiExperiment Viewer | ||
|Analysis and Visualization of Microarray Data | |Analysis and Visualization of Microarray Data | ||
|TIGR | |TIGR | ||
|JAVA | |JAVA | ||
| + | |- | ||
! TreeArrange and Treeps | ! TreeArrange and Treeps | ||
|Software for displaying and manipulating hierarchical clustered data | |Software for displaying and manipulating hierarchical clustered data | ||
Latest revision as of 14:10, 2 November 2007
| Program | Description | Platform |
|---|---|---|
| GSEA | Determines if a given set of genes shows differences between two biological states | JAVA |
| GeneCluster | Self-organizing maps | JAVA, Windows NT |
| Connectivity Map | Uses pattern-matching algorithms to enable discovery of functional connections between drugs, genes, and diseases | Web |
| GeneCruiser | Annotation tool for Affymetrix probes | Web |
| 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 |
| 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 |
| GEDA | Gene expression data analysis and simulation tools, offering a variety of options for processing and analyzing results. | University of Pittsburgh and UPMC | Web |
| GenMAPP | Tools for visualizing data from gene expression experiments in the context of biological pathways. | Conklin lab; Gladstone Institute & the UCSF | Windows |
| GeneX | Gene Expression Database : integrated toolset for data analysis and comparison | National Center for Genome Resources | Windows, Linux, SunOS/Solaris |
| 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 |
