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ACNE is a tool to estimate allele-specific copy numbers (CNs) in Affymetrix SNP array data. The ACNE algorithm uses the cross hybridization probe data. ACNE is a part of the Aroma project. See links below.


Genetics; genetic variation


  • Operation: Variation detection
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU Lesser General Public License v2.1
  • Cost: Free
  • Version name: 3.2.0
  • Maturity: Stable
  • Credit: University of Navarra, Fundación para la Investigación Médica Aplicada.
  • Contact: arubio _at_
  • Collection: Aroma


Ortiz-Estevez M, Bengtsson H, Rubio A "ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays." Bioinformatics. 2010 Aug 1;26(15):1827-33. Epub 2010 Jun 6.
PMID: 20529889
PMCID: PMC2913655

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