GenePattern
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| Developer(s) | Broad Institute |
|---|---|
| Stable release | 3.9.2 / March 2015 |
| Operating system | Windows: XP, Vista, Windows 7, Windows 8;
Mac: OS 10.7 and later Unix: Linux, Ubuntu, SuSE, CentOS |
| License | proprietary |
| Website | www |
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 23,000 registered users at over 2900 commercial and non-profit organizations internationally.
Usage
GenePattern is a powerful scientific workflow system that provides access to more than 220 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:
- As a free public web server,[1] supported by the Broad Institute. Users can create logins, save histories, and create pipelines on the server.
- As open-source software that can be downloaded and installed locally.[2]
- Public web servers hosted by other organizations.[3]
- As part of the GenomeSpace initiative.
See also
- Genome Compiler - an all-in-one software platform for DNA design & visualization, data management and collaboration.
- GenePattern Public Server - a publicly hosted instance of GenePattern utilizing the Broad Institute's compute farm as the back end.
Notes
References
- GenePattern 2.0 Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo & Jill P. Mesirov. Nature Genetics - 38, 500 - 501 (2006)
External links
Related software:
