@article{hughesman2016robust,
  title={{A Robust Protocol for Using Multiplexed Droplet Digital PCR to Quantify Somatic Copy Number Alterations in Clinical Tissue Specimens}},
  author={Hughesman, Curtis B and Lu, XJ David and Liu, Kelly YP and Zhu, Yuqi and Poh, Catherine F and Haynes, Charles},
  journal={PloS one},
  volume={11},
  number={8},
  pages={e0161274},
  year={2016},
  publisher={Public Library of Science}
}

@article{hindson2011high,
  title={{High-throughput droplet digital PCR system for absolute quantitation of DNA copy number}},
  author={Hindson, Benjamin J and Ness, Kevin D and Masquelier, Donald A and Belgrader, Phillip and Heredia, Nicholas J and Makarewicz, Anthony J and Bright, Isaac J and Lucero, Michael Y and Hiddessen, Amy L and Legler, Tina C and others},
  journal={Analytical chemistry},
  volume={83},
  number={22},
  pages={8604--8610},
  year={2011},
  publisher={ACS Publications}
}

@article{malek2015flowdensity,
  title={{flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification}},
  author={Malek, Mehrnoush and Taghiyar, Mohammad Jafar and Chong, Lauren and Finak, Greg and Gottardo, Raphael and Brinkman, Ryan R},
  journal={Bioinformatics},
  volume={31},
  number={4},
  pages={606--607},
  year={2015},
  publisher={Oxford Univ Press}
}

@article{ge2012flowpeaks,
  title={{flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding}},
  author={Ge, Yongchao and Sealfon, Stuart C},
  journal={Bioinformatics},
  volume={28},
  number={15},
  pages={2052--2058},
  year={2012},
  publisher={Oxford Univ Press}
}

@article{zare2010data,
  title={{Data reduction for spectral clustering to analyze high throughput flow cytometry data}},
  author={Zare, Habil and Shooshtari, Parisa and Gupta, Arvind and Brinkman, Ryan R},
  journal={BMC bioinformatics},
  volume={11},
  number={1},
  pages={403},
  year={2010},
  publisher={BioMed Central}
}

@book{papadimitriou1982combinatorial,
  title={{Combinatorial optimization: algorithms and complexity}},
  author={Papadimitriou, Christos H and Steiglitz, Kenneth},
  year={1982},
  publisher={Courier Corporation}
}

@article{hanahan2011hallmarks,
  title={{Hallmarks of cancer: the next generation}},
  author={Hanahan, Douglas and Weinberg, Robert A},
  journal={cell},
  volume={144},
  number={5},
  pages={646--674},
  year={2011},
  publisher={Elsevier}
}

@article{hubert1985comparing,
  title={{Comparing partitions}},
  author={Hubert, Lawrence and Arabie, Phipps},
  journal={Journal of classification},
  volume={2},
  number={1},
  pages={193--218},
  year={1985},
  publisher={Springer}
}

@article{hornik2005clue,
  title={{A clue for cluster ensembles}},
  author={Hornik, Kurt},
  journal={Journal of Statistical Software},
  volume={14},
  number={12},
  pages={1--25},
  year={2005},
  publisher={University of California, Los Angeles}
}

@Manual{shiny2017,
    title = {{shiny: Web Application Framework for R}},
    author = {Winston Chang and Joe Cheng and JJ Allaire and Yihui Xie and Jonathan McPherson},
    year = {2017},
    note = {R package version 1.0.3},
    url = {https://CRAN.R-project.org/package=shiny},
  }
  
  @article{trypsteen2015ddpcrquant,
  title={{ddpcRquant: threshold determination for single channel droplet digital PCR experiments}},
  author={Trypsteen, Wim and Vynck, Matthijs and De Neve, Jan and Bonczkowski, Pawel and Kiselinova, Maja and Malatinkova, Eva and Vervisch, Karen and Thas, Olivier and Vandekerckhove, Linos and De Spiegelaere, Ward},
  journal={Analytical and bioanalytical chemistry},
  volume={407},
  number={19},
  pages={5827},
  year={2015},
  publisher={Springer Science \& Business Media}
}

@article{attali2016ddpcr,
  title={{ddpcr: an R package and web application for analysis of droplet digital PCR data}},
  author={Attali, Dean and Bidshahri, Roza and Haynes, Charles and Bryan, Jennifer},
  journal={F1000Research},
  volume={5},
  year={2016},
  publisher={Faculty of 1000 Ltd}
}

@article{chiu2017twoddpcr,
  title={{twoddpcr: An R/Bioconductor package and Shiny app for Droplet Digital PCR analysis}},
  author={Chiu, Anthony and Ayub, Mahmood and Dive, Caroline and Brady, Ged and Miller, Crispin J},
  journal={Bioinformatics},
  pages={btx308},
  year={2017},
  publisher={Oxford University Press}
}

@article{mahalanobis,
  title={{On the generalised distance in statistics}},
  author={Mahalanobis, Prasanta Chandra},
  journal={Proceedings of the National Institute of Sciences of India},
  pages={49--55},
  year={1936}
}
