@Manual{allaire2020rmarkdown,
  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 = {2020},
  note = {R package version 2.1},
  url = {https://github.com/rstudio/rmarkdown},
}

@Manual{boettiger2019knitcitations,
  title = {knitcitations: Citations for 'Knitr' Markdown Files},
  author = {Carl Boettiger},
  year = {2019},
  note = {R package version 1.0.10},
  url = {https://CRAN.R-project.org/package=knitcitations},
}

@Article{colladotorres2016regionreport,
  author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
  title = {regionReport: Interactive reports for region-level and feature-level genomic analyses [version2; referees: 2 approved, 1 approved with reservations]},
  journal = {F1000Research},
  year = {2016},
  doi = {10.12688/f1000research.6379.2},
  url = {http://f1000research.com/articles/4-105/v2},
  volume = {4},
  pages = {105},
}

@Manual{kolde2019pheatmap,
  title = {pheatmap: Pretty Heatmaps},
  author = {Raivo Kolde},
  year = {2019},
  note = {R package version 1.0.12},
  url = {https://CRAN.R-project.org/package=pheatmap},
}

@Article{love2014moderated,
  title = {Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
  author = {Michael I. Love and Wolfgang Huber and Simon Anders},
  year = {2014},
  journal = {Genome Biology},
  doi = {10.1186/s13059-014-0550-8},
  volume = {15},
  issue = {12},
  pages = {550},
}

@Manual{neuwirth2014rcolorbrewer,
  title = {RColorBrewer: ColorBrewer Palettes},
  author = {Erich Neuwirth},
  year = {2014},
  note = {R package version 1.1-2},
  url = {https://CRAN.R-project.org/package=RColorBrewer},
}

@Book{wickham2016ggplot2,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2016},
  isbn = {978-3-319-24277-4},
  url = {https://ggplot2.tidyverse.org},
}

@InCollection{xie2014knitr,
  booktitle = {Implementing Reproducible Computational Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}

@Book{xie2018markdown,
  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},
}

@Manual{xie2020wrapper,
  title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
  author = {Yihui Xie and Joe Cheng and Xianying Tan},
  year = {2020},
  note = {R package version 0.13},
  url = {https://CRAN.R-project.org/package=DT},
}