GenePattern: Home

GenePattern is a powerful genomic analysis platform that provides access to more than 180 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

Learn to use GenePattern in 10 minutes:
Learn hands-on with the Quick Start tutorial
Learn by watching short video tutorials

Run analyses on the Broad public server
Use GenePattern to run analyses on a server at the Broad Institute.

Download GenePattern
GenePattern runs on Windows, Mac, and Linux.

RNA-seq Suite

GenePattern now offers a suite of tools to support a wide variety of RNA-seq analyses, including short-read mapping, identification of splice junctions, transcript and isoform detection, quantitation, and differential expression. Please see the overview for more information.

Modules from Recent Publications

StrandSpecRNASeqEval by Levin et al. (Nature Methods, 2010)

Microsoft Word add-in for the GenePattern Reproducible Research Document (GRRD), by Mesirov (Science, 2010)

AuDIT by Abbatiello et al. (Clinical Chemistry, 2010)

FLAME by Pyne et al. (PNAS, 2009)

ESPPredictor by Fusaro et al. (Nature Biotechnology, 2009)

all modules...

What's New

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GenePattern at ISMB 2012

GenePattern will be featured at the Bioinformatics Software Interoperability SIG at ISMB on July 13 in Long Beach, CA.

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