packages.bib

@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 = {2024},
  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 = {2024},
  note = {R package version 2.66.0},
  url = {https://bioconductor.org/packages/Biobase},
  doi = {10.18129/B9.bioc.Biobase},
}

@Manual{R-BiocGenerics,
  title = {BiocGenerics: S4 generic functions used in Bioconductor},
  author = {{The Bioconductor Dev Team} and Hervé Pagès},
  year = {2025},
  note = {R package version 0.53.5},
  url = {https://bioconductor.org/packages/BiocGenerics},
}

@Manual{R-BiocStyle,
  title = {BiocStyle: Standard styles for vignettes and other Bioconductor documents},
  author = {Andrzej Oleś},
  year = {2024},
  note = {R package version 2.34.0},
  url = {https://bioconductor.org/packages/BiocStyle},
  doi = {10.18129/B9.bioc.BiocStyle},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2024},
  note = {R package version 0.34.2},
  url = {https://github.com/rstudio/bookdown},
}

@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-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-generics,
  title = {generics: Common S3 Generics not Provided by Base R Methods Related to
Model Fitting},
  author = {Hadley Wickham and Max Kuhn and Davis Vaughan},
  year = {2022},
  note = {R package version 0.1.3},
  url = {https://generics.r-lib.org},
}

@Manual{R-GenomeInfoDb,
  title = {GenomeInfoDb: Utilities for manipulating chromosome names, including modifying
them to follow a particular naming style},
  author = {Sonali Arora and Martin Morgan and Marc Carlson and Hervé Pagès},
  year = {2024},
  note = {R package version 1.42.1},
  url = {https://bioconductor.org/packages/GenomeInfoDb},
  doi = {10.18129/B9.bioc.GenomeInfoDb},
}

@Manual{R-GenomicRanges,
  title = {GenomicRanges: Representation and manipulation of genomic intervals},
  author = {Patrick Aboyoun and Hervé Pagès and Michael Lawrence},
  year = {2024},
  note = {R package version 1.58.0},
  url = {https://bioconductor.org/packages/GenomicRanges},
  doi = {10.18129/B9.bioc.GenomicRanges},
}

@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 and Teun {van den Brand}},
  year = {2024},
  note = {R package version 3.5.1},
  url = {https://ggplot2.tidyverse.org},
}

@Manual{R-gridExtra,
  title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
  author = {Baptiste Auguie},
  year = {2017},
  note = {R package version 2.3},
  url = {https://CRAN.R-project.org/package=gridExtra},
}

@Manual{R-hexbin,
  title = {hexbin: Hexagonal Binning Routines},
  author = {Dan Carr and Nicholas Lewin-Koh and Martin Maechler},
  year = {2024},
  note = {R package version 1.28.5},
  url = {https://github.com/edzer/hexbin},
}

@Manual{R-IRanges,
  title = {IRanges: Foundation of integer range manipulation in Bioconductor},
  author = {Hervé Pagès and Patrick Aboyoun and Michael Lawrence},
  year = {2024},
  note = {R package version 2.40.1},
  url = {https://bioconductor.org/packages/IRanges},
  doi = {10.18129/B9.bioc.IRanges},
}

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2024},
  note = {R package version 1.49},
  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 = {2024},
  note = {R package version 1.9.4},
  url = {https://lubridate.tidyverse.org},
}

@Manual{R-magrittr,
  title = {magrittr: A Forward-Pipe Operator for R},
  author = {Stefan Milton Bache and Hadley Wickham},
  year = {2022},
  note = {R package version 2.0.3},
  url = {https://magrittr.tidyverse.org},
}

@Manual{R-MatrixGenerics,
  title = {MatrixGenerics: S4 Generic Summary Statistic Functions that Operate on
Matrix-Like Objects},
  author = {Constantin Ahlmann-Eltze and Peter Hickey and Hervé Pagès},
  year = {2025},
  note = {R package version 1.18.1},
  url = {https://bioconductor.org/packages/MatrixGenerics},
  doi = {10.18129/B9.bioc.MatrixGenerics},
}

@Manual{R-matrixStats,
  title = {matrixStats: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)},
  author = {Henrik Bengtsson},
  year = {2025},
  note = {R package version 1.5.0},
  url = {https://github.com/HenrikBengtsson/matrixStats},
}

@Manual{R-msmbstyle,
  title = {msmbstyle: MSMB Styles for R Markdown Documents},
  author = {Mike Smith},
  year = {2024},
  note = {R package version 0.0.22, commit b3d4ad8eaf46eb111d711cc600f9e258dd7a6807},
  url = {https://github.com/lgatto/msmbstyle},
}

@Manual{R-patchwork,
  title = {patchwork: The Composer of Plots},
  author = {Thomas Lin Pedersen},
  year = {2024},
  note = {R package version 1.3.0},
  url = {https://patchwork.data-imaginist.com},
}

@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 = {2024},
  note = {R package version 2.1.5},
  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 = {2024},
  note = {R package version 2.29},
  url = {https://github.com/rstudio/rmarkdown},
}

@Manual{R-rWSBIM1207,
  title = {rWSBIM1207: Companion Package for WSBIM1207 Course},
  author = {Laurent Gatto},
  year = {2024},
  note = {R package version 0.1.19, commit 3561033e7a99182664a0a20f603382b5539941f0},
  url = {https://github.com/UCLouvain-CBIO/rWSBIM1207},
}

@Manual{R-rWSBIM1322,
  title = {rWSBIM1322: Companion Package for WSBIM1322 Course},
  author = {Laurent Gatto},
  year = {2024},
  note = {R package version 0.3.2, commit 782af41b081c3b900bf3575fe2bc6e8f3619b323},
  url = {https://github.com/UCLouvain-CBIO/rWSBIM1322},
}

@Manual{R-S4Vectors,
  title = {S4Vectors: Foundation of vector-like and list-like containers in
Bioconductor},
  author = {Hervé Pagès and Michael Lawrence and Patrick Aboyoun},
  year = {2024},
  note = {R package version 0.44.0},
  url = {https://bioconductor.org/packages/S4Vectors},
  doi = {10.18129/B9.bioc.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-SummarizedExperiment,
  title = {SummarizedExperiment: A container (S4 class) for matrix-like assays},
  author = {Martin Morgan and Valerie Obenchain and Jim Hester and Hervé Pagès},
  year = {2024},
  note = {R package version 1.36.0},
  url = {https://bioconductor.org/packages/SummarizedExperiment},
  doi = {10.18129/B9.bioc.SummarizedExperiment},
}

@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{GenomicRanges2013,
  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{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/},
}

@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},
}