GenePattern is a powerful genomic analysis platform that provides access to hundreds of 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
Version: 3.8.2 (Jun 23, 2014)
GenePattern runs on Windows, Mac, and Linux.

GenePattern Team Blog

Changes to Startup Env Impact R Modules on Broad Hosted Servers: As a result of the software update on August 14, we modified the startup environment for the server. This was necessary because the server now requires Java 7. It was previously using Java 6. Surprisingly, this necessitated a change to the R configuration. You may notice slight changes to the behavior of your R modules. For example, the ATLANTISInputs module failed with this error message:

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Updated GPARC

GPARC (The GenePattern Module Archive)  has a new look! We also added and improved features. Visit the User Guide for more information.

GPARC is a repository and community where GenePattern users can share and discuss their own modules. You can now upload your modules directly from your own GenePattern server to GPARC. Read more in our User Guide.

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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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 GenePattern is a BioIT World Best Practices award winner.