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hsegHMM
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hsegHMM

hsegHMM is a software tool to analyze copy number variation (CNV). The hsegHMM algorithm uses a hidden Markov model (HMM) as the basis that includes hypersegmentation and an E-M method.



hsegHMM

hsegHMM is a software tool to analyze copy number variation (CNV). The hsegHMM algorithm uses a hidden Markov model (HMM) as the basis that includes hypersegmentation and an E-M method.

Topic

Genetics; DNA structural variation; Oncology

Details

  • Operation: Polymorphism detection; Sequence analysis; Structural variation detection
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU GPL v2
    • Cost: Free
  • Version name: 0.0.4
    • Maturity: Stable
  • Credit: The Intramural Research Program of US National Institutes of Health, National Cancer Institute.
  • Contact: Hyoyoung Choo-Wosoba hyoyoung.choo-wosoba _at_ nih.gov
  • Collection: -

Publications

Choo-Wosoba H, Albert PS, Zhu B "hsegHMM: hidden Markov model-based allele-specific copy number alteration analysis accounting for hypersegmentation." BMC Bioinformatics. 2018 Nov 14;19(1):424. https://doi.org/10.1186/s12859-018-2412-y
PMID: 30428830
PMCID: PMC6236906


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