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qpure

qpure

An R script that uses copy-number and B allele frequency data from Illumina Omni 1M genotyping (SNP) arrays to assess the tumour content (cellularity) of cancer tissue samples.

Topic

Biology, Genetics, DNA polymorphism

Details

  • Operation: Modelling and simulation
  • Software interface: Command-line interface
  • Language: R
  • Operating system: Linux, Mac OS X
  • License: Not stated
  • Cost: Free
  • Version name: 1.1
  • Credit: Song S, Nones K, Miller D, Harliwong I, Kassahn KS, Pinese M, Pajic M, Gill AJ, Johns AL, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Newell F, Cowley MJ, Wu J, Wilson P, Fink L, Biankin AV, Waddell N, Grimmond SM, Pearson JV.
  • Contact: Sarah Song s.song _at_ imb.uq.edu.au, Sean M. Grimmond s.grimmond _at_ imb.uq.edu.au
  • Collection: -

Publications

Song S, Nones K, Miller D, Harliwong I, Kassahn KS, Pinese M, Pajic M, Gill AJ, Johns AL, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Newell F, Cowley MJ, Wu J, Wilson P, Fink L, Biankin AV, Waddell N, Grimmond SM, Pearson JV "qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles." PLoS ONE 2012; 7(9):e45835 https://doi.org/10.1371/journal.pone.0045835
PMID: 23049875
PMCID: PMC3457972


Download and documentation




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