Suvarna Garge (Editor)

GenePattern

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Developer(s)
  
Broad Institute

License
  
BSD

Stable release
  
3.9.8 / June 2016

Website
  
www.genepattern.org

Operating system
  
Windows: XP, Vista, Windows 7, Windows 8; Mac: OS 10.7 and laterUnix: Linux, Ubuntu, SuSE, CentOS

GenePattern is a freely available computational biology open-source software package developed at the Broad Institute of MIT and Harvard for the analysis of genomic data. Designed to enable researchers to develop, capture, and reproduce genomic analysis methodologies, GenePattern was first released in 2004. It now has over 45,000 registered users at over 2900 commercial and non-profit organizations internationally.

Contents

Usage

GenePattern is a powerful scientific workflow system that provides access to more than 250 genomic analysis tools. Use the analysis tools as building blocks to design sophisticated analysis pipelines that capture the methods, parameters and data used to produce analysis results. Pipelines can be used to create, edit and share reproducible in silico results.

Features

  • regularly updated repository of computational analysis modules that support data preprocessing, gene expression analysis, proteomics, Single nucleotide polymorphism (SNP) analysis, flow cytometry, and next-generation sequencing
  • pipelines that allow you to chain modules together to create analysis workflows
  • tools to support easy creation and integration of new analysis modules
  • versioning of modules and pipelines to ensure reproducible research
  • web browser, application, and programmatic interfaces to make analysis modules and pipelines available to a broad range of users

    • Availability

    GenePattern is available:

    1. As a free public web server, supported by the Broad Institute. Users can create logins, save histories, and create pipelines on the server.
    2. As open-source software that can be downloaded and installed locally.
    3. Public web servers hosted by other organizations.
    4. As part of the GenomeSpace initiative.

    References

    GenePattern Wikipedia
    (Text) CC BY-SA


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