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

Detail

  • Operation: Copy number estimation

  • Software interface: Web user interface

  • Language: Javascript;R;C++;PHP

  • 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.

  • Input: -

  • Output: -

  • Contact: mschatz@cshl.edu

  • Collection: -

  • Maturity: -

Publications

  • Interactive analysis and assessment of single-cell copy-number variations
  • Garvin T, et al. Interactive analysis and assessment of single-cell copy-number variations. Interactive analysis and assessment of single-cell copy-number variations. 2015; 12:1058-60. doi: 10.1038/nmeth.3578
  • https://doi.org/10.1038/nmeth.3578
  • PMID: 26344043
  • PMC: PMC4775251

Download and documentation

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