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CNVtools

CNVtools

CNVtools is an R package designed for testing of copy number variation (CNV) data to facilitate association studies.

Topic

Genetic variation; Sequencing

Details

  • Operation: Copy number estimation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v3
  • Cost: Free
  • Version name: 1.78.0
  • Maturity: Stable
  • Credit: The National Institute of General Medical Sciences, Juvenile Diabetes Research Foundation (JDRF), JDRF/WT fellowship, Wellcome Trust Case Control Consortium.
  • Contact: christopher.barnes _at_ imperial.ac.uk
  • Collection: BioConductor

Publications

Barnes C, Plagnol V, Fitzgerald T, Redon R, Marchini J, Clayton D, Hurles ME "A robust statistical method for case-control association testing with copy number variation." Nat Genet. 2008 Oct;40(10):1245-52. https://doi.org/10.1038/ng.206
PMID: 18776912
PMCID: PMC2784596


Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590


Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600


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