GenePattern
Encyclopedia
GenePattern is a freely available software package developed at the Broad Institute
Broad Institute
The Broad Institute is a genomic medicine research center located in Cambridge, Massachusetts, United States. Although it is independently governed and supported as a 501 nonprofit research organization, the institute is formally affiliated with the Massachusetts Institute of Technology, Harvard...
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 15,000 registered users at over 2300 commercial and non-profit organizations internationally.
Usage
GenePattern is a powerful scientific workflow platform that provides access to more than 150 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 expressionGene expressionGene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
analysis, proteomicsProteomicsProteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
, and Single nucleotide polymorphismSingle nucleotide polymorphismA single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome differs between members of a biological species or paired chromosomes in an individual...
(SNP) analysis - 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
See also
GenePattern Public Server - a publicly hosted instance of GenePattern utilizing the Broad InstituteBroad Institute
The Broad Institute is a genomic medicine research center located in Cambridge, Massachusetts, United States. Although it is independently governed and supported as a 501 nonprofit research organization, the institute is formally affiliated with the Massachusetts Institute of Technology, Harvard...
's compute farm as the back end.
External links
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