Data Analysis Resources

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The following softwares are available at Whitehead Institute for Data Analysis (More to be added soon):

Genepix Whitehead Only
GenePix Pro is the complete standalone image analysis software for microarrays, tissue arrays and cell arrays. We currently have 3 network licences for the software. You can download the software from axon website and install it on your PC. Genepix does NOT have a mac version.

Agilent Feature Extraction Whitehead Only
Agilent's Feature Extraction 9.5.3 Software reads and processes up to 100 raw microarray image files in an automated, walkaway mode. The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. Application-specific QC reports summarize multiple analyses. Installed on the analysis computer in Rm 327, 9CC.

Bioconductor Free
Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data. Bioconductor is primarily based on the R programming language but we do accept contributions in any programming language. It can read the genepix as well as agilent feature extraction and affymetrix data files directly. A certain level of programming experience is required.

dChip Free
A program developed by Wing Wang's lab at Harvard known as DNA-Chip Analyzer (dChip). dChip is a model-based analysis of oligonucleotide (Affymetrix) expression arrays that uses a probe-sensitivity index to capture the response characteristic of a specific probe pair and calculates model-based expression indexes. dChip is described in Genome Biol. 2001;2(8):RESEARCH0032 and J Cell Biochem Suppl 2001;Suppl 37:120-5.

Affymetrix analysis tools Free
The NetAffx- Analysis Center is the most comprehensive resource of integrated array contents and functional annotations available. The flexible query capabilities provided help you retrieve biological information for specific probe sets. Go to this web site and register to use the annotation tool.

Affymetrix also has a Gene Ontology (GO) tool. Gene Ontology (Ashburner, Ball et al. 2000). The Gene Ontology Mining Tool maps GeneChip probe sets to these hierarchical vocabularies. In addition to providing the GO terms for annotated genes, it provides graphical, interactive views of probe set representation within the biological process, molecular function, or cellular component hierarchies.

Cluster Free
A program developed by Michael Eisen for the analysis of gene expression data using hierarchical clustering, self-organizing maps (SOMs), k-means clustering, and principal component analysis. Hierarchical clustering methods described in Eisen et al. (1998) PNAS 95:14863.

TreeView Free
A program developed by Michael Eisen for visualization of the results of microarray data analysis. One can graphically browse results of clustering and other analyses from Cluster. Supports tree-based and image based browsing of hierarchical trees. Multiple output formats for generation of images for publications.

BaRC analysis tools Whitehead Only
A set of web based tools for general analysis, sequence extraction, annotation (limited species), Homology and functional analysis

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