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exomeCopy R package is for detection of copy number variants (CNV) from exome and unpaired sample sequencing. The implementation is based on a hidden Markov model on background read depth and GC-content to normalize copy count.


Exome sequencing


  • Operation: Copy number estimation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v2+
  • Cost: Free
  • Version name: 1.30.0
  • Maturity: Stable
  • Credit: European Union’s Seventh Framework Program under grant agreement number 241995, project GENCODYS.
  • Contact: michaelisaiahlove _at_
  • Collection: BioConductor


Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA "Modeling read counts for CNV detection in exome sequencing data." Stat Appl Genet Mol Biol. 2011 Nov 8;10(1). pii: /j/sagmb.2011.10.issue-1/1544-6115.1732/1544-6115.1732.xml.
PMID: 23089826
PMCID: PMC3517018

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.
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.
PMID: 15461798
PMCID: PMC545600

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