CGHcall

CGHcall boosts the accuracy of array CGH data analysis by utilizing breakpoint information from segmentation and incorporating several overlooked biological concepts. The algorithm is proven to be effective through simulations and real data testing, with an increased ability to identify single-copy gains and amplifications by incorporating more than three classes. Additionally, CGHcall enables the factoring of chromosome arm information into the analysis.

Topic

Oncology

Detail

  • Operation: Nucleic acid sequence analysis

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: -

  • Cost: Free

  • Version name: 2.60.0

  • Credit: Center for Medical Systems Biology (CMSB), established by the Netherlands Genomics Initiative / Netherlands Organization for Scientific Research.

  • Input: -

  • Output: -

  • Contact: Mark van de Wiel mark.vdwiel@vumc.nl

  • Collection: -

  • Maturity: Mature

Publications

  • CGHcall: calling aberrations for array CGH tumor profiles.
  • van de Wiel MA, et al. CGHcall: calling aberrations for array CGH tumor profiles. CGHcall: calling aberrations for array CGH tumor profiles. 2007; 23:892-4. doi: 10.1093/bioinformatics/btm030
  • https://doi.org/10.1093/bioinformatics/btm030
  • PMID: 17267432
  • PMC: -

Download and documentation

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