analysis_ref.bib

@article{dante,
  title={DAnTE: a statistical tool for quantitative analysis of-omics data},
  author={Polpitiya, Ashoka D and Qian, Wei-Jun and Jaitly, Navdeep and Petyuk, Vladislav A and Adkins, Joshua N and Camp, David G and Anderson, Gordon A and Smith, Richard D},
  journal={Bioinformatics},
  volume={24},
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  pages={1556--1558},
  year={2008},
  publisher={Oxford University Press}
}

@article{spans,
  title={A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors},
  author={Webb-Robertson, Bobbie-Jo M and Matzke, Melissa M and Jacobs, Jon M and Pounds, Joel G and Waters, Katrina M},
  journal={Proteomics},
  volume={11},
  number={24},
  pages={4736--4741},
  year={2011},
  publisher={Wiley Online Library}
}

 @Manual{emmeans,
    title = {emmeans: Estimated Marginal Means, aka Least-Squares Means},
    author = {Russell Lenth},
    year = {2019},
    note = {R package version 1.3.3},
    url = {https://CRAN.R-project.org/package=emmeans},
  }
  
@article{rmd,
  title={Improved quality control processing of peptide-centric LC-MS proteomics data},
  author={Matzke, Melissa M and Waters, Katrina M and Metz, Thomas O and Jacobs, Jon M and Sims, Amy C and Baric, Ralph S and Pounds, Joel G and Webb-Robertson, Bobbie-Jo M},
  journal={Bioinformatics},
  volume={27},
  number={20},
  pages={2866--2872},
  year={2011},
  publisher={Oxford University Press}
}

@article{sppca,
  title={Sequential projection pursuit principal component analysis--dealing with missing data associated with new-omics technologies},
  author={Webb-Robertson, Bobbie-Jo M and Matzke, Melissa M and Metz, Thomas O and McDermott, Jason E and Walker, Hyunjoo and Rodland, Karin D and Pounds, Joel G and Waters, Katrina M},
  journal={Biotechniques},
  volume={54},
  number={3},
  pages={165--168},
  year={2013},
  publisher={Future Science}
}


 @Manual{R,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2018},
    url = {https://www.R-project.org/},
  }


 @Book{ggplot,
    author = {Hadley Wickham},
    title = {ggplot2: Elegant Graphics for Data Analysis},
    publisher = {Springer-Verlag New York},
    year = {2016},
    isbn = {978-3-319-24277-4},
    url = {http://ggplot2.org},
  }
  
  @Manual{dplyr,
    title = {dplyr: A Grammar of Data Manipulation},
    author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
    year = {2018},
    note = {R package version 0.7.6},
    url = {https://CRAN.R-project.org/package=dplyr},
  }
  
@Article{lme4,
    title = {Fitting Linear Mixed-Effects Models Using {lme4}},
    author = {Douglas Bates and Martin M{\"a}chler and Ben Bolker and Steve Walker},
    journal = {Journal of Statistical Software},
    year = {2015},
    volume = {67},
    number = {1},
    pages = {1--48},
    doi = {10.18637/jss.v067.i01},
  }

@article{pmartr,
  title={pmartR: Quality Control and Statistics for Mass Spectrometry-based Biological Data},
  author={Stratton, Kelly G and Webb-Robertson, Bobbie-Jo M and McCue, Lee Ann and Claborne, Daniel and Stanfill, Bryan and Godinez, Iobani and Johansen, Thomas and Thompson, Allison M and Burnum-Johnson, Kristin E and Waters, Katrina M and Bramer, Lisa M},
  journal={Journal of proteome research},
  year={2019},
  publisher={ACS Publications}
}

  @Manual{trelliscopejs,
    title = {trelliscopejs: Create Interactive Trelliscope Displays},
    author = {Ryan Hafen and Barret Schloerke},
    year = {2019},
    note = {R package version 0.1.18},
    url = {https://github.com/hafen/trelliscopejs},
  }
  
  @Manual{purrr,
    title = {purrr: Functional Programming Tools},
    author = {Lionel Henry and Hadley Wickham},
    year = {2018},
    note = {R package version 0.2.5},
    url = {https://CRAN.R-project.org/package=purrr},
  }
  
  @article{webb2010combined,
  title={Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data},
  author={Webb-Robertson, Bobbie-Jo M and McCue, Lee Ann and Waters, Katrina M and Matzke, Melissa M and Jacobs, Jon M and Metz, Thomas O and Varnum, Susan M and Pounds, Joel G},
  journal={Journal of proteome research},
  volume={9},
  number={11},
  pages={5748--5756},
  year={2010},
  publisher={ACS Publications}
}