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paper.bib
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@Manual{r-core,
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/},
}
@Article{phyloseq,
author = {P McMurdie and S Holmes},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
volume = {8},
number = {4},
year = {2013},
doi = {10.1371/journal.pone.0061217},
url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
@Article{metacoder,
title = {Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.},
author = {Z Foster and T Sharpton and N Grünwald},
journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
year = {2017},
month = {02},
volume = {13},
pages = {1-15},
number = {2},
doi = {10.1371/journal.pcbi.1005404},
url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005404},
}
@Manual{taxa,
title = {Taxa: An R package implementing data standards and methods for taxonomic data.},
author = {Z Foster and S Chamberlain and N Grünwald},
journal = {F1000Research},
year = {2018},
volume = {7},
number = {272},
doi = {10.12688/f1000research.14013.2},
url = {https://f1000research.com/articles/7-272/v2},
}
@Article{qiime,
title = {QIIME allows analysis of high-throughput community sequencing data.},
author = {J Caporaso and J Kuczynski and J Stombaugh and K Bittinger and F Bushman and E Costello and N Fierer
and A Gonzalez Pena and J Goodrich and J Gordon and G Huttley and S Kelley and D Knights
and J Koenig and R Ley and C Lozupone and D McDonald and B Muegge and M Pirrung and J Reeder
and J Sevinsky and P Turnbaugh and W Walters and J Widmann and T Yatsunenko and J Zaneveld
and R Knight},
journal = {Nature Methods},
year = {2010},
volume = {7},
pages = {335-336},
doi = {10.1038/nmeth.f.303},
url = {qiime.org},
}
@Article{silva_1,
title = {The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.},
author = {C Quast and E Pruesse and P Yilmaz and J Gerken and T Schweer and P Yarza and J Peplies and F Glöckner},
journal = {Nucleic Acids Research},
year = {2013},
issue = {41},
pages = {D590-D596},
doi = {10.1093/nar/gks1219},
}
@Article{silva_2,
title = {The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks.},
author = {P Yilmaz and L Parfrey and P Yarza and J Gerken and E Pruesse and C Quast
and T Schweer and J Peplies and W Ludwig and F Glöckner},
journal = {Nucleic Acids Research},
year = {2014},
volume = {42},
issue = {D1},
pages = {D643-D648},
doi = {10.1093/nar/gkt1209},
}
@Manual{microbiome,
title = {microbiome: Tools for microbiome analysis in R},
author = {L Lahti and S Shetty and T Blake and J Salojarvi},
year = {2017},
note = {R package version 1.5.28},
url = {http://microbiome.github.com/microbiome},
}