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BubbleTree is an R package for analysis of tumor samples in next generation sequencing (NGS) data. The BubbleTree algorithm can estimate cancer causing cell inpurity, ploidy, clonality, and allele-sepcific copy number variation (CNV). It displays the results in a graph format. The Authors claim that BubbleTree out performs THetA2, ABSOLUTE, AbsCN-seq and ASCAT tools.


Genetics; whole genome sequencing; Oncology


  • Operation: Sample comparison; variant calling; 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: 2.14.0
  • Maturity: Stable
  • Credit: MedImmune/AstraZeneca.
  • Contact: creasyt _at_;weizhu365 _at_
  • Collection: BioConductor


Zhu W, Kuziora M, Creasy T, Lai Z, Morehouse C, Guo X, Sebastian Y, Shen D, Huang J, Dry JR, Xue F, Jiang L, Yao Y, Higgs BW "BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality using next generation sequencing data." Nucleic Acids Res. 2016 Feb 29;44(4):e38.
PMID: 26578606
PMCID: PMC4770205

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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