bibtexlib.bib

@article{callahan2016dada2,
  title={DADA2: high-resolution sample inference from Illumina amplicon data},
  author={Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P},
  journal={Nature methods},
  volume={13},
  number={7},
  pages={581},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{simpson1949measurement,
  title={Measurement of diversity},
  author={Simpson, Edward H},
  journal={nature},
  volume={163},
  number={4148},
  pages={688},
  year={1949},
  publisher={Nature Publishing Group},
  doi={10.1038/163688a0}
}

@article{hill1973diversity,
  title={Diversity and evenness: a unifying notation and its consequences},
  author={Hill, Mark O},
  journal={Ecology},
  volume={54},
  number={2},
  pages={427--432},
  year={1973},
  publisher={Wiley Online Library},
  URL={https://doi.org/10.2307/1934352}
}

@article{foster2018taxa,
  title={Taxa: An R package implementing data standards and methods for taxonomic data},
  author={Foster, Zachary SL and Chamberlain, Scott and Gr{\"u}nwald, Niklaus J},
JOURNAL = {F1000Research},
VOLUME = {7},
YEAR = {2018},
NUMBER = {272},
DOI = {10.12688/f1000research.14013.1}
}

@article{mcmurdie2013phyloseq,
  title={phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data},
  author={McMurdie, Paul J and Holmes, Susan},
  journal={PloS One},
  volume={8},
  number={4},
  pages={e61217},
  year={2013},
  url={https://doi.org/10.1371/journal.pone.0061217},
  publisher={Public Library of Science}
}

@article{comeau2017microbiome,
  title={Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research},
  author={Comeau, Andr{\'e} M and Douglas, Gavin M and Langille, Morgan GI},
  journal={mSystems},
  volume={2},
  number={1},
  pages={e00127--16},
  year={2017},
  url={http://msystems.asm.org/content/2/1/e00127-16},
  publisher={Am Soc Microbiol}
}

@article{lozupone2005unifrac,
  title={UniFrac: a new phylogenetic method for comparing microbial communities},
  author={Lozupone, Catherine and Knight, Rob},
  journal={Applied and Environmental Microbiology},
  volume={71},
  number={12},
  pages={8228--8235},
  year={2005},
  url={http://aem.asm.org/content/71/12/8228.full},
  publisher={Am Soc Microbiol}
}

@article{foster2017metacoder,
  title={Metacoder: An R package for visualization and manipulation of community taxonomic diversity data},
  author={Foster, Zachary SL and Sharpton, Thomas J and Gr{\"u}nwald, Niklaus J},
  journal={PLoS Computational Biology},
  volume={13},
  number={2},
  pages={e1005404},
  year={2017},
  url={https://doi.org/10.1371/journal.pcbi.1005404},
  publisher={Public Library of Science}
}

@article{edgar2013uparse,
  title={UPARSE: highly accurate OTU sequences from microbial amplicon reads},
  author={Edgar, Robert C},
  journal={Nature Methods},
  volume={10},
  number={10},
  pages={996--998},
  year={2013},
  url={http://dx.doi.org/10.1038/nmeth.2604},
  publisher={Nature Research}
}

@article{dixon2003vegan,
  title={VEGAN, a package of R functions for community ecology},
  author={Dixon, Philip},
  journal={Journal of Vegetation Science},
  volume={14},
  number={6},
  pages={927--930},
  year={2003},
  publisher={BioOne}
}

@article{oksanen2007vegan,
    title = {vegan: Community Ecology Package},
    author = {Jari Oksanen and F. Guillaume Blanchet and Michael Friendly and Roeland Kindt and Pierre Legendre and Dan McGlinn and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner},
    year = {2018},
    note = {R package version 2.5-1},
    url = {https://CRAN.R-project.org/package=vegan}
}

@article{schloss2009introducing,
  title={Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities},
  author={Schloss, Patrick D and Westcott, Sarah L and Ryabin, Thomas and Hall, Justine R and Hartmann, Martin and Hollister, Emily B and Lesniewski, Ryan A and Oakley, Brian B and Parks, Donovan H and Robinson, Courtney J and others},
  journal={Applied and Environmental Microbiology},
  volume={75},
  number={23},
  pages={7537--7541},
  year={2009},
  url={http://aem.asm.org/cgi/pmidlookup?view=long&pmid=19801464},
  publisher={Am Soc Microbiol}
}

@article{caporaso2010qiime,
  title={QIIME allows analysis of high-throughput community sequencing data},
  author={Caporaso, J Gregory and Kuczynski, Justin and Stombaugh, Jesse and Bittinger, Kyle and Bushman, Frederic D and Costello, Elizabeth K and Fierer, Noah and Pe{\~n}a, Antonio Gonzalez and Goodrich, Julia K and Gordon, Jeffrey I and others},
  journal={Nature Methods},
  volume={7},
  number={5},
  pages={335--336},
  year={2010},
  url={https://www.nature.com/articles/nmeth.f.303},
  publisher={Nature Publishing Group}
}

@article{whittaker1960vegetation,
  title={Vegetation of the Siskiyou mountains, Oregon and California},
  author={Whittaker, Robert Harding},
  journal={Ecological monographs},
  volume={30},
  number={3},
  pages={279--338},
  year={1960},
  publisher={Wiley Online Library}
}

@article{wagner2016host,
  title={Host genotype and age shape the leaf and root microbiomes of a wild perennial plant},
  author={Wagner, Maggie R and Lundberg, Derek S and Tijana, G and Tringe, Susannah G and Dangl, Jeffery L and Mitchell-Olds, Thomas},
  journal={Nature communications},
  volume={7},
  pages={12151},
  year={2016},
  publisher={Nature Publishing Group},
  doi={10.1038/ncomms12151}
}

@article{zeeberg2004mistaken,
  title={Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics},
  author={Zeeberg, Barry R and Riss, Joseph and Kane, David W and Bussey, Kimberly J and Uchio, Edward and Linehan, W Marston and Barrett, J Carl and Weinstein, John N},
  journal={BMC bioinformatics},
  volume={5},
  number={1},
  pages={80},
  year={2004},
  publisher={BioMed Central},
  URL={https://doi.org/10.1186/1471-2105-5-80}
}

@article{wickham2015dplyr,
  title={dplyr: A grammar of data manipulation},
  author={Wickham, Hadley and Francois, Romain},
  journal={R package version 0.4},
  volume={3},
  year={2015}
}

@Book{wickham2009ggplot2,
    author = {Hadley Wickham},
    title = {ggplot2: Elegant Graphics for Data Analysis},
    publisher = {Springer-Verlag New York},
    year = {2009},
    isbn = {978-0-387-98140-6},
    url = {http://ggplot2.org},
  }
  
@article{callahan2017exact,
  title={Exact sequence variants should replace operational taxonomic units in marker-gene data analysis},
  author={Callahan, Benjamin J and McMurdie, Paul J and Holmes, Susan P},
  journal={The ISME journal},
  volume={11},
  number={12},
  pages={2639},
  year={2017},
  publisher={Nature Publishing Group}
}