packages.bib

@Manual{R-AnnotationDbi,
  title = {AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor},
  author = {Hervé Pagès and Marc Carlson and Seth Falcon and Nianhua Li},
  year = {2022},
  note = {R package version 1.58.0},
  url = {https://bioconductor.org/packages/AnnotationDbi},
}

@Manual{R-base,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2022},
  url = {https://www.R-project.org/},
}

@Manual{R-Biobase,
  title = {Biobase: Base functions for Bioconductor},
  author = {R. Gentleman and V. Carey and M. Morgan and S. Falcon},
  year = {2022},
  note = {R package version 2.56.0},
  url = {https://bioconductor.org/packages/Biobase},
}

@Manual{R-BiocGenerics,
  title = {BiocGenerics: S4 generic functions used in Bioconductor},
  author = {The Bioconductor Dev Team},
  year = {2022},
  note = {R package version 0.42.0},
  url = {https://bioconductor.org/packages/BiocGenerics},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2023},
  note = {R package version 0.36},
  url = {https://github.com/rstudio/bookdown},
}

@Manual{R-clusterProfiler,
  title = {clusterProfiler: A universal enrichment tool for interpreting omics data},
  author = {Guangchuang Yu},
  year = {2022},
  note = {R package version 4.4.4},
  url = {https://yulab-smu.top/biomedical-knowledge-mining-book/},
}

@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller and Davis Vaughan},
  year = {2023},
  note = {R package version 1.1.4},
  url = {https://dplyr.tidyverse.org},
}

@Manual{R-DT,
  title = {DT: A Wrapper of the JavaScript Library DataTables},
  author = {Yihui Xie and Joe Cheng and Xianying Tan},
  year = {2023},
  note = {R package version 0.30},
  url = {https://github.com/rstudio/DT},
}

@Manual{R-enrichplot,
  title = {enrichplot: Visualization of Functional Enrichment Result},
  author = {Guangchuang Yu},
  year = {2022},
  note = {R package version 1.16.2},
  url = {https://yulab-smu.top/biomedical-knowledge-mining-book/},
}

@Manual{R-forcats,
  title = {forcats: Tools for Working with Categorical Variables (Factors)},
  author = {Hadley Wickham},
  year = {2023},
  note = {R package version 1.0.0},
  url = {https://forcats.tidyverse.org/},
}

@Manual{R-ggplot2,
  title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
  author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington},
  year = {2023},
  note = {R package version 3.4.4},
  url = {https://ggplot2.tidyverse.org},
}

@Manual{R-IRanges,
  title = {IRanges: Foundation of integer range manipulation in Bioconductor},
  author = {H. Pagès and P. Aboyoun and M. Lawrence},
  year = {2022},
  note = {R package version 2.30.1},
  url = {https://bioconductor.org/packages/IRanges},
}

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2023},
  note = {R package version 1.45},
  url = {https://yihui.org/knitr/},
}

@Manual{R-lubridate,
  title = {lubridate: Make Dealing with Dates a Little Easier},
  author = {Vitalie Spinu and Garrett Grolemund and Hadley Wickham},
  year = {2023},
  note = {R package version 1.9.3},
  url = {https://lubridate.tidyverse.org},
}

@Manual{R-matrixTests,
  title = {matrixTests: Fast Statistical Hypothesis Tests on Rows and Columns of
Matrices},
  author = {Karolis Koncevičius},
  year = {2023},
  note = {R package version 0.2.3},
  url = {https://github.com/karoliskoncevicius/matrixTests},
}


@Manual{R-pathview,
  title = {pathview: a tool set for pathway based data integration and visualization},
  author = {Weijun Luo},
  year = {2022},
  note = {R package version 1.36.1},
  url = {https://github.com/datapplab/pathview},
}

@Manual{R-purrr,
  title = {purrr: Functional Programming Tools},
  author = {Hadley Wickham and Lionel Henry},
  year = {2023},
  note = {R package version 1.0.2},
  url = {https://purrr.tidyverse.org/},
}

@Manual{R-readr,
  title = {readr: Read Rectangular Text Data},
  author = {Hadley Wickham and Jim Hester and Jennifer Bryan},
  year = {2023},
  note = {R package version 2.1.4},
  url = {https://readr.tidyverse.org},
}

@Manual{R-rmarkdown,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Yihui Xie and Christophe Dervieux 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 = {2023},
  note = {R package version 2.25},
  url = {https://github.com/rstudio/rmarkdown},
}

@Manual{R-S4Vectors,
  title = {S4Vectors: Foundation of vector-like and list-like containers in
Bioconductor},
  author = {H. Pagès and M. Lawrence and P. Aboyoun},
  year = {2022},
  note = {R package version 0.34.0},
  url = {https://bioconductor.org/packages/S4Vectors},
}

@Manual{R-stringr,
  title = {stringr: Simple, Consistent Wrappers for Common String Operations},
  author = {Hadley Wickham},
  year = {2023},
  note = {R package version 1.5.1},
  url = {https://stringr.tidyverse.org},
}

@Manual{R-tibble,
  title = {tibble: Simple Data Frames},
  author = {Kirill Müller and Hadley Wickham},
  year = {2023},
  note = {R package version 3.2.1},
  url = {https://tibble.tidyverse.org/},
}

@Manual{R-tidyr,
  title = {tidyr: Tidy Messy Data},
  author = {Hadley Wickham and Davis Vaughan and Maximilian Girlich},
  year = {2024},
  note = {R package version 1.3.1},
  url = {https://tidyr.tidyverse.org},
}

@Manual{R-tidyverse,
  title = {tidyverse: Easily Install and Load the Tidyverse},
  author = {Hadley Wickham},
  year = {2023},
  note = {R package version 2.0.0},
  url = {https://tidyverse.tidyverse.org},
}

@Article{Biobase2015,
  author = {W. Huber and V. J. Carey and R. Gentleman and S. Anders and M. Carlson and B. S. Carvalho and H. C. Bravo and S. Davis and L. Gatto and T. Girke and R. Gottardo and F. Hahne and K. D. Hansen and R. A. Irizarry and M. Lawrence and M. I. Love and J. MacDonald and V. Obenchain and A. K. {Ole's} and H. {Pag`es} and A. Reyes and P. Shannon and G. K. Smyth and D. Tenenbaum and L. Waldron and M. Morgan},
  title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
  journal = {Nature Methods},
  year = {2015},
  volume = {12},
  number = {2},
  pages = {115--121},
  url = {http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html},
}

@Article{BiocGenerics2015,
  author = {{Huber} and {W.} and {Carey} and V. J. and {Gentleman} and {R.} and {Anders} and {S.} and {Carlson} and {M.} and {Carvalho} and B. S. and {Bravo} and H. C. and {Davis} and {S.} and {Gatto} and {L.} and {Girke} and {T.} and {Gottardo} and {R.} and {Hahne} and {F.} and {Hansen} and K. D. and {Irizarry} and R. A. and {Lawrence} and {M.} and {Love} and M. I. and {MacDonald} and {J.} and {Obenchain} and {V.} and {{Ole's}} and A. K. and {{Pag`es}} and {H.} and {Reyes} and {A.} and {Shannon} and {P.} and {Smyth} and G. K. and {Tenenbaum} and {D.} and {Waldron} and {L.} and {Morgan} and {M.}},
  title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
  journal = {Nature Methods},
  year = {2015},
  volume = {12},
  number = {2},
  pages = {115--121},
  url = {http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html},
}

@Book{bookdown2016,
  title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2016},
  isbn = {978-1138700109},
  url = {https://bookdown.org/yihui/bookdown},
}

@Article{clusterProfiler2021,
  title = {clusterProfiler 4.0: A universal enrichment tool for interpreting omics data},
  author = {Tianzhi Wu and Erqiang Hu and Shuangbin Xu and Meijun Chen and Pingfan Guo and Zehan Dai and Tingze Feng and Lang Zhou and Wenli Tang and Li Zhan and xiaochong Fu and Shanshan Liu and Xiaochen Bo and Guangchuang Yu},
  journal = {The Innovation},
  year = {2021},
  volume = {2},
  number = {3},
  pages = {100141},
  doi = {10.1016/j.xinn.2021.100141},
}

@Article{clusterProfiler2012,
  title = {clusterProfiler: an R package for comparing biological themes among gene clusters},
  author = {Guangchuang Yu and Li-Gen Wang and Yanyan Han and Qing-Yu He},
  journal = {OMICS: A Journal of Integrative Biology},
  year = {2012},
  volume = {16},
  number = {5},
  pages = {284-287},
  pmid = {22455463},
  doi = {10.1089/omi.2011.0118},
}

@Book{ggplot22016,
  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},
}

@Article{IRanges2013,
  title = {Software for Computing and Annotating Genomic Ranges},
  author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es and Patrick Aboyoun and Marc Carlson and Robert Gentleman and Martin Morgan and Vincent Carey},
  year = {2013},
  journal = {{PLoS} Computational Biology},
  volume = {9},
  issue = {8},
  doi = {10.1371/journal.pcbi.1003118},
  url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118},
}

@Book{knitr2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {https://yihui.org/knitr/},
}

@InCollection{knitr2014,
  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},
}

@Article{lubridate2011,
  title = {Dates and Times Made Easy with {lubridate}},
  author = {Garrett Grolemund and Hadley Wickham},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {40},
  number = {3},
  pages = {1--25},
  url = {https://www.jstatsoft.org/v40/i03/},
}

@Article{pathview2013,
  author = {{Luo} and {Weijun} and {Brouwer} and {Cory}},
  title = {Pathview: an R/Bioconductor package for pathway-based data integration and visualization},
  journal = {Bioinformatics},
  year = {2013},
  doi = {10.1093/bioinformatics/btt285},
  volume = {29},
  number = {14},
  pages = {1830-1831},
}

@Book{rmarkdown2018,
  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},
  isbn = {9781138359338},
  url = {https://bookdown.org/yihui/rmarkdown},
}

@Book{rmarkdown2020,
  title = {R Markdown Cookbook},
  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2020},
  isbn = {9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}

@Article{tidyverse2019,
  title = {Welcome to the {tidyverse}},
  author = {Hadley Wickham and Mara Averick and Jennifer Bryan and Winston Chang and Lucy D'Agostino McGowan and Romain François and Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
  year = {2019},
  journal = {Journal of Open Source Software},
  volume = {4},
  number = {43},
  pages = {1686},
  doi = {10.21105/joss.01686},
}