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paper.bib
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@article{rmarkdown,
title = {rmarkdown: Dynamic Documents for R},
author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang},
year = {2018},
note = {R package version 1.10},
url = {https://CRAN.R-project.org/package=rmarkdown},
}
@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/},
}
@article{Casadevall2016,
doi = {10.1128/mbio.01256-16},
url = {https://doi.org/10.1128/mbio.01256-16},
year = {2016},
month = {aug},
publisher = {American Society for Microbiology},
volume = {7},
number = {4},
pages = {e01256--16},
author = {Arturo Casadevall and Lee M. Ellis and Erika W. Davies and Margaret McFall-Ngai and Ferric C. Fang},
title = {A Framework for Improving the Quality of Research in the Biological Sciences},
journal = {{mBio}}
}
@article{Collins2014,
doi = {10.1038/505612a},
url = {https://doi.org/10.1038/505612a},
year = {2014},
month = {jan},
publisher = {Springer Nature},
volume = {505},
number = {7485},
pages = {612--613},
author = {Francis S. Collins and Lawrence A. Tabak},
title = {{NIH} plans to enhance reproducibility},
journal = {Nature}
}
@article{Garijo2013,
doi = {10.1371/journal.pone.0080278},
url = {https://doi.org/10.1371/journal.pone.0080278},
year = {2013},
month = {nov},
publisher = {Public Library of Science ({PLOS})},
volume = {8},
number = {11},
pages = {e80278},
author = {Daniel Garijo and Sarah Kinnings and Li Xie and Lei Xie and Yinliang Zhang and Philip E. Bourne and Yolanda Gil},
editor = {Christos A. Ouzounis},
title = {Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome},
journal = {{PLOS} {ONE}}
}
@article{Kozich2013,
doi = {10.1128/aem.01043-13},
url = {https://doi.org/10.1128/aem.01043-13},
year = {2013},
month = {jun},
publisher = {American Society for Microbiology},
volume = {79},
number = {17},
pages = {5112--5120},
author = {James J. Kozich and Sarah L. Westcott and Nielson T. Baxter and Sarah K. Highlander and Patrick D. Schloss},
title = {Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the {MiSeq} Illumina Sequencing Platform},
journal = {Applied and Environmental Microbiology}
}
@article{Noble2009,
doi = {10.1371/journal.pcbi.1000424},
url = {https://doi.org/10.1371/journal.pcbi.1000424},
year = {2009},
month = {jul},
publisher = {Public Library of Science ({PLOS})},
volume = {5},
number = {7},
pages = {e1000424},
author = {William Stafford Noble},
editor = {Fran Lewitter},
title = {A Quick Guide to Organizing Computational Biology Projects},
journal = {{PLOS} Computational Biology}
}
@article{Ravel2014,
doi = {10.1186/2049-2618-2-8},
url = {https://doi.org/10.1186/2049-2618-2-8},
year = {2014},
publisher = {Springer Nature},
volume = {2},
number = {1},
pages = {8},
author = {Jacques Ravel and K Wommack},
title = {All hail reproducibility in microbiome research},
journal = {Microbiome}
}
@article{Schloss2009,
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},
publisher={Am Soc Microbiol}
}
@article{Schloss2018,
doi = {10.1128/mbio.00525-18},
url = {https://doi.org/10.1128/mbio.00525-18},
year = {2018},
month = {jun},
publisher = {American Society for Microbiology},
volume = {9},
number = {3},
pages = {e00525--18},
author = {Patrick D. Schloss},
editor = {Jacques Ravel},
title = {Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research},
journal = {{mBio}}
}