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 | [ image quantification software ] |
| Scanalyze | Stanford software used for processing fuorescent microarray images. Includes semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database. |
| F-Scan | NIH software for quantifying fluorescent images. F-Scan requires MATLAB software and a UNIX account. Analyses include scatterplots, multiple image comparison, data merging. |
| P-Scan | NIH software for quantifying peak intensities from images generated from membranes scanned using a phosphoimager. P-Scan requires MATLAB software access and a UNIX account. |
| [ data analysis software ] |
| SAM: Significance Analysis of Microarrays | An excel add-in that supports supervised learning for genomic expression data mining (uses data permutations to provide estimate of False Discovery Rate for multiple testing). |
| BioConductor | Bioconductor is an open source and open development software project based primarily on the R programming language created to provide tools for the analysis and comprehension of genomic data. |
| dChip | DNA-Chip Analyzer (dChip) is a software package implementing model-based expression analysis of oligonucleotide arrays and several high-level analysis procedures (particularly useful for Affymetrix arrays). High-level analysis in dChip includes comparative analysis, hierarchical clustering, SNP analysis etc. (Li and Wong, 2001 [Pubmed]) |
| GenePattern | GenePattern is a software package from the Broad Institute for the analysis of molecular profiles, e.g., genome-wide microarray expression signatures. It includes a collection of analytic and visualization tools, interfaces for the easy construction of analytic pipelines and integration of new modules without additional programming |
| Expression Profiler | A collection of EBI web accessible microarray data analysis tools including clustering and gene ontology tools. |
| Cluster and TreeView | Classic cluster analysis and graphical visualization software from Eisen lab at Stanford. Currently includes hierarchical clustering, self-organizing maps (SOMs), k-means clustering, principal component analysis.Hierarchical clustering methods described in Eisen et al. (1998) PNAS 95:14863. |
| CAGED | CAGED (Cluster Analysis of Gene Expression Dynamics) is a computer program for the analysis of temporal gene expression data. CAGED is based on a method called Bayesian Clustering by Dynamics, which identifies the most probable set of clusters given a set of time series (it can be used as a Bayesian clustering program on a-temporal expression data). |
| Cyber-T | Cyber-T is a a microarray analysis web interface from UCI's Institute for Genomics and Bioinformatics. It accommodates both paired (2-dye) data and data in which control and experiment are on separate experiments (e.g. affymetrix based data). It also supports Bayesian statistical approaches and Bonferroni corrections for significance analysis of differentially expressed clones. GeneX database and analysis tools are written in R and can also be installed locally. |
| TM4 (TIGR) | A package of open source software programs for microarray analysis from J. Craig Venter Institute. The suite includes MIDAS (Microarray Data Analysis System), MADAM (MicroArray DAta Manager), MEV (MultiExperiment Viewer) and the image processing tool Spotfinder. |
| SNOMAD | A collection of algorithms written in R statistical language, directed at the normalization and standardization of DNA microarray data. Useful mostly for paired microarray data. |
| BRB Array Tools | Integrated microsoft excel add-in useful for visualization and statistical analysis of DNA microarray data. Genes can also be annotated by linking to NCBI databases using clone identifiers. |
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| [ functional analysis software ] |
| DAVID and EASE (NIH) |
DAVID (Database for Annotation, Visualization and Integrated Discovery) and EASE (the Expression Analysis Systematic Explorer)provide integrated solutions for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteomic platforms. |
| Cytoscape | Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. |
| Onto-Express | Onto-Express systematically translates genetic fingerprints into functional profiles. Using strings of accession or cluster identification numbers, Onto-Express searches the public databases and returns tables that correlate expression profiles with the cytogenetic gene locations, the biochemical and molecular functions, the biological processes, cellular components and cellular roles of the translated proteins. |
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| [ selected links to academic core facilities ] |
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