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Ginkgo
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Ginkgo

A web-based tool for the analysis of single-cell copy-number variations (CNVs). It compiles copy number profiles from mapped reads and constructs phylogenetic trees of related cells.



Ginkgo

A web-based tool for the analysis of single-cell copy-number variations (CNVs). It compiles copy number profiles from mapped reads and constructs phylogenetic trees of related cells.

Topic

Genetics; Sequence analysis; DNA structural variation

Details

  • Operation: Copy number estimation
  • Software interface: Web user interface
  • Language: Javascript;R;C++;PHP
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: BSD 2-Clause "Simplified" License
    • Cost: Free
  • Version name: -
  • Credit: The US National Institutes of Health award (R01-HG006677) to MCS, the US National Science Foundation (DBI-1350041) to MCS, the Cold Spring Harbor Laboratory (CSHL) Cancer Center Support Grant (5P30CA045508), and by the Watson School of Biological Sciences at CSHL through a Training Grant (5T32GM065094) from the US National Institutes of Health.
  • Contact: mschatz _at_ cshl.edu
  • Collection: -

Publications

Garvin T, Aboukhalil R, Kendall J, Baslan T, Atwal GS, Hicks J, Wigler M, Schatz MC "Interactive analysis and assessment of single-cell copy-number variations" Nat Methods. 2015 Nov;12(11):1058-60. https://doi.org/10.1038/nmeth.3578
PMID: 26344043
PMCID: PMC4775251


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