book.bib

@article{BeaulieuJones2017,
  doi = {10.1038/nbt.3780},
  url = {https://doi.org/10.1038/nbt.3780},
  year = {2017},
  month = mar,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {35},
  number = {4},
  pages = {342--346},
  author = {Brett K Beaulieu-Jones and Casey S Greene},
  title = {Reproducibility of computational workflows is automated using continuous analysis},
  journal = {Nature Biotechnology}
}
@Manual{rmarkdown2021,
  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 and Richard Iannone},
  year = {2021},
  note = {R package version 2.10},
  url = {https://github.com/rstudio/rmarkdown},
}

@Book{Xie2018,
  title = {R Markdown: The Definitive Guide},
  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2018},
  note = {ISBN 9781138359338},
  url = {https://bookdown.org/yihui/rmarkdown},
}

@Book{Xie2020,
  title = {R Markdown Cookbook},
  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2020},
  note = {ISBN 9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}

@article{mangul2019,
  title = {Challenges and recommendations to improve the installability and archival stability of omics computational tools},
  author = {Mangul, Serghei and Mosqueiro, Thiago and Abdill, Richard J and Duong, Dat and Mitchell, Keith and Sarwal, Varuni and Hill, Brian and Brito, Jaqueline and Littman, Russell Jared and Statz, Benjamin and others},
  journal = {PLoS Biology},
  volume = {17},
  number = {6},
  pages = {e3000333},
  year = {2019},
  publisher = {Public Library of Science San Francisco, CA USA}
}

@article{gardner2022,
  title={Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software},
  author={Gardner, Paul P and Paterson, James M and McGimpsey, Stephanie and Ashari-Ghomi, Fatemeh and Umu, Sinan U and Pawlik, Aleksandra and Gavryushkin, Alex and Black, Michael A},
  journal={Genome Biology},
  volume={23},
  number={1},
  pages={1--13},
  year={2022},
  publisher={BioMed Central}
}