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AneuFinder

AneuFinder

AneuFinder is an R package for copy number variation (CNV) detection, breakpoint detection, karyotype, and heterogeneity analysis between single cells.

Topic

Sequencing; Genomics; Genetics

Details

  • Operation: Copy number estimation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Artistic-2.0
  • Cost: Free
  • Version name: 1.12.1
  • Maturity: Stable
  • Credit: Dutch Cancer Society grant (KWF grant RUG-2012-5549) and a Groningen Foundation for Paediatric Oncology (SKOG) grant to FF and PML, and by an NWO (The Netherlands Organisation for Scientific Research) MEERVOUD grant and a University of Groningen Rosalind Franklin Fellowship grant to MCT.
  • Contact: aaron.taudt _at_ gmail.com f.foijer _at_ umcg.nl
  • Collection: BioConductor

Publications

Bakker B, Taudt A, Belderbos ME, Porubsky D, Spierings DC, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A, de Bont ES, van den Berg A, Guryev V, Lansdorp PM, Colomé-Tatché M, Foijer F "Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies." Genome Biol. 2016 May 31;17(1):115. https://doi.org/10.1186/s13059-016-0971-7
PMID: 27246460
PMCID: PMC4888588


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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