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GenePattern
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GenePattern

GenePattern is a web-based tool that includes PEPPeR (Platform for Experimental Proteomics Pattern Recognition) and several other algorithms, such as 'Landmark Matching' and 'Peak Matching'. It also includes Jupyter Notebooks and analysis pipelines



GenePattern

GenePattern is a web-based tool that includes PEPPeR (Platform for Experimental Proteomics Pattern Recognition) and several other algorithms, such as 'Landmark Matching' and 'Peak Matching'. It also includes Jupyter Notebooks and analysis pipelines

Topic

Functional genomics; Proteomics; Proteomics experiment

Details

  • Operation: Copy number estimation; Clustering; Pathway or network analysis; Expression analysis; Genetic variation analysis
  • Software interface: Web user interface
  • Language: Java
  • Operating system: Linux; Mac OS X
  • License: Other
    • Cost: Free
  • Version name: 3.9.11
  • Credit: The National Institutes of Health (NIH), The Gates Foundation, The Entertainment Industry Foundation, the United States Department of Energy (DOE).
  • Contact: mesirov _at_ broad.mit.edu
  • Collection: -

Publications

Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA "PEPPeR, a platform for experimental proteomic pattern recognition." Mol. Cell Proteomics 2006; 5(10):1927-41 https://doi.org/10.1074/mcp.M600222-MCP200
PMID: 16857664
PMCID: PMC2649820


Mah CK, Wenzel AT, Juarez EF, Tabor T, Reich MM, Mesirov JP "An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data." F1000Res https://doi.org/10.12688/f1000research.15830.1
PMID: 31316748
PMCID: PMC6611141


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