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GenePattern is a powerful genomic analysis platform that provides access to more than 240 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

Getting Started

quickstartLearn to use GenePattern in 10 minutes:
Learn hands-on with the Quick Start tutorial
Learn by watching short video tutorials
onlineRun analyses on the Broad public server
Use GenePattern to run analyses on a server at the Broad Institute.
download Download GenePattern
GenePattern runs on Windows, Mac, and Linux.

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 SNP6 Copy Number Inference Pipeline

The CopyNumberInferencePipeline is a method for analyzing your Affymetrix SNP6.0 data files in GenePattern.  For more information, please view our online documentation.
Citing GenePattern
Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501
Google Scholar | CiteULike | more...
National Cancer Institute NIGMS

Funded by the National Cancer Institute and the National Institute of General Medical Sciences.
GenomeSpace GenePattern is participating in the GenomeSpace initiative.
 

best practices award Winner of the Editor's Choice award for the 2005 BioIT World Best Practices competition.