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conumee is a set of processing and plotting methods for making copy-number variation (CNV) analysis using Illumina 450k and EPIC methylation arrays.


Microarray experiment; Epigenetics; Sequence analysis


  • Operation: Copy number estimation
  • Input: Microarray hybridisation data; IDAT; BED; Text; Sequence coordinates; IDAT; BED; Text
  • Output: Plot; text; nucleic acid features; text
  • 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: 1.8.0
  • Credit: -
  • Contact: conumee _at_
  • Collection: BioConductor


Mah CK, Mesirov JP, Chavez L "An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays." F1000Res. 2018 Dec 5;7. pii: ISCB Comm J-1897.
PMID: 31105932
PMCID: PMC6498745

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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