packages.bib

@Manual{R-airway,
  title = {airway: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle
cells, by Himes et al PLoS One 2014},
  author = {Michael Love},
  year = {2024},
  note = {R package version 1.26.0},
  url = {https://bioconductor.org/packages/airway},
  doi = {10.18129/B9.bioc.airway},
}

@Manual{R-annotate,
  title = {annotate: Annotation for microarrays},
  author = {Jeff Gentry},
  year = {2024},
  note = {R package version 1.84.0},
  url = {https://bioconductor.org/packages/annotate},
  doi = {10.18129/B9.bioc.annotate},
}

@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 = {2024},
  note = {R package version 1.68.0},
  url = {https://bioconductor.org/packages/AnnotationDbi},
  doi = {10.18129/B9.bioc.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 = {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},
  year = {2024},
  note = {R package version 0.52.0},
  url = {https://bioconductor.org/packages/BiocGenerics},
  doi = {10.18129/B9.bioc.BiocGenerics},
}

@Manual{R-BiocIO,
  title = {BiocIO: Standard Input and Output for Bioconductor Packages},
  author = {Martin Morgan and Michael Lawrence and Daniel {Van Twisk}},
  year = {2024},
  note = {R package version 1.16.0},
  url = {https://bioconductor.org/packages/BiocIO},
  doi = {10.18129/B9.bioc.BiocIO},
}

@Manual{R-BiocParallel,
  title = {BiocParallel: Bioconductor facilities for parallel evaluation},
  author = {Martin Morgan and Jiefei Wang and Valerie Obenchain and Michel Lang and Ryan Thompson and Nitesh Turaga},
  year = {2024},
  note = {R package version 1.40.0},
  url = {https://bioconductor.org/packages/BiocParallel},
  doi = {10.18129/B9.bioc.BiocParallel},
}

@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-bioDist,
  title = {bioDist: Different distance measures},
  author = {B. Ding and R. Gentleman and Vincent Carey},
  year = {2024},
  note = {R package version 1.78.0},
  url = {https://bioconductor.org/packages/bioDist},
  doi = {10.18129/B9.bioc.bioDist},
}

@Manual{R-Biostrings,
  title = {Biostrings: Efficient manipulation of biological strings},
  author = {Hervé Pagès and Patrick Aboyoun and Robert Gentleman and Saikat DebRoy},
  year = {2024},
  note = {R package version 2.74.0},
  url = {https://bioconductor.org/packages/Biostrings},
  doi = {10.18129/B9.bioc.Biostrings},
}

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

@Manual{R-BSgenome,
  title = {BSgenome: Software infrastructure for efficient representation of full
genomes and their SNPs},
  author = {Hervé Pagès},
  year = {2024},
  note = {R package version 1.74.0},
  url = {https://bioconductor.org/packages/BSgenome},
  doi = {10.18129/B9.bioc.BSgenome},
}

@Manual{R-BSgenome.Dmelanogaster.UCSC.dm2,
  title = {BSgenome.Dmelanogaster.UCSC.dm2: Full genome sequences for Drosophila melanogaster (UCSC version
dm2)},
  author = {The Bioconductor Dev Team},
  year = {2014},
  note = {R package version 1.4.0},
}

@Manual{R-class,
  title = {class: Functions for Classification},
  author = {Brian Ripley},
  year = {2023},
  note = {R package version 7.3-22},
  url = {http://www.stats.ox.ac.uk/pub/MASS4/},
}

@Manual{R-cluster,
  title = {cluster: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.},
  author = {Martin Maechler and Peter Rousseeuw and Anja Struyf and Mia Hubert},
  year = {2023},
  note = {R package version 2.1.6},
  url = {https://svn.r-project.org/R-packages/trunk/cluster/},
}

@Manual{R-ComplexHeatmap,
  title = {ComplexHeatmap: Make Complex Heatmaps},
  author = {Zuguang Gu},
  year = {2024},
  note = {R package version 2.22.0},
  url = {https://bioconductor.org/packages/ComplexHeatmap},
  doi = {10.18129/B9.bioc.ComplexHeatmap},
}

@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-factoextra,
  title = {factoextra: Extract and Visualize the Results of Multivariate Data Analyses},
  author = {Alboukadel Kassambara and Fabian Mundt},
  year = {2020},
  note = {R package version 1.0.7},
  url = {http://www.sthda.com/english/rpkgs/factoextra},
}

@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-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 1.42.0},
  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-ggbeeswarm,
  title = {ggbeeswarm: Categorical Scatter (Violin Point) Plots},
  author = {Erik Clarke and Scott Sherrill-Mix and Charlotte Dawson},
  year = {2023},
  note = {R package version 0.7.2},
  url = {https://github.com/eclarke/ggbeeswarm},
}

@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-Hmisc,
  title = {Hmisc: Harrell Miscellaneous},
  author = {Harrell, Jr., Frank E},
  year = {2024},
  note = {R package version 5.2-0},
  url = {https://hbiostat.org/R/Hmisc/},
}

@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 2.40.0},
  url = {https://bioconductor.org/packages/IRanges},
  doi = {10.18129/B9.bioc.IRanges},
}

@Manual{R-KernSmooth,
  title = {KernSmooth: Functions for Kernel Smoothing Supporting Wand \& Jones (1995)},
  author = {Matt Wand},
  year = {2024},
  note = {R package version 2.23-24},
  url = {https://CRAN.R-project.org/package=KernSmooth},
}

@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-lattice,
  title = {lattice: Trellis Graphics for R},
  author = {Deepayan Sarkar},
  year = {2024},
  note = {R package version 0.22-6},
  url = {https://lattice.r-forge.r-project.org/},
}

@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-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 = {2024},
  note = {R package version 1.18.0},
  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 = {2024},
  note = {R package version 1.4.1},
  url = {https://github.com/HenrikBengtsson/matrixStats},
}

@Manual{R-MLInterfaces,
  title = {MLInterfaces: Uniform interfaces to R machine learning procedures for data in
Bioconductor containers},
  author = {Vincent Carey and Jess Mar},
  year = {2024},
  note = {R package version 1.86.0},
  url = {https://bioconductor.org/packages/MLInterfaces},
  doi = {10.18129/B9.bioc.MLInterfaces},
}

@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-MSnbase,
  title = {MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics},
  author = {Laurent Gatto and Johannes Rainer and Sebastian Gibb},
  year = {2024},
  note = {R package version 2.32.0},
  url = {https://bioconductor.org/packages/MSnbase},
  doi = {10.18129/B9.bioc.MSnbase},
}

@Manual{R-MultiAssayExperiment,
  title = {MultiAssayExperiment: Software for the integration of multi-omics experiments in
Bioconductor},
  author = {Marcel Ramos and Martin Morgan and Vincent J Carey and Levi Waldron},
  year = {2024},
  note = {R package version 1.32.0},
  url = {https://bioconductor.org/packages/MultiAssayExperiment},
  doi = {10.18129/B9.bioc.MultiAssayExperiment},
}

@Manual{R-mzR,
  title = {mzR: parser for netCDF, mzXML and mzML and mzIdentML files (mass
spectrometry data)},
  author = {Steffen Neumann and Laurent Gatto and Qiakng Kou},
  year = {2024},
  note = {R package version 2.40.0},
  url = {https://bioconductor.org/packages/mzR},
  doi = {10.18129/B9.bioc.mzR},
}

@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-plotly,
  title = {plotly: Create Interactive Web Graphics via plotly.js},
  author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
  year = {2024},
  note = {R package version 4.10.4},
  url = {https://plotly-r.com},
}

@Manual{R-pRoloc,
  title = {pRoloc: A unifying bioinformatics framework for spatial proteomics},
  author = {Laurent Gatto and Lisa Breckels and Oliver Crook},
  year = {2024},
  note = {R package version 1.46.0},
  url = {https://bioconductor.org/packages/pRoloc},
  doi = {10.18129/B9.bioc.pRoloc},
}

@Manual{R-pRolocdata,
  title = {pRolocdata: Data accompanying the pRoloc package},
  author = {Laurent Gatto and Oliver Crook and Lisa Breckels},
  year = {2024},
  note = {R package version 1.44.0},
  url = {https://bioconductor.org/packages/pRolocdata},
  doi = {10.18129/B9.bioc.pRolocdata},
}

@Manual{R-ProtGenerics,
  title = {ProtGenerics: Generic infrastructure for Bioconductor mass spectrometry
packages},
  author = {Laurent Gatto and Johannes Rainer},
  year = {2024},
  note = {R package version 1.38.0},
  url = {https://bioconductor.org/packages/ProtGenerics},
  doi = {10.18129/B9.bioc.ProtGenerics},
}

@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-QFeatures,
  title = {QFeatures: Quantitative features for mass spectrometry data},
  author = {Laurent Gatto and Christophe Vanderaa},
  year = {2024},
  note = {R package version 1.16.0},
  url = {https://bioconductor.org/packages/QFeatures},
  doi = {10.18129/B9.bioc.QFeatures},
}

@Manual{R-Rcpp,
  title = {Rcpp: Seamless R and C++ Integration},
  author = {Dirk Eddelbuettel and Romain Francois and JJ Allaire and Kevin Ushey and Qiang Kou and Nathan Russell and Iñaki Ucar and Doug Bates and John Chambers},
  year = {2024},
  note = {R package version 1.0.13-1},
  url = {https://www.rcpp.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-rtracklayer,
  title = {rtracklayer: R interface to genome annotation files and the UCSC genome
browser},
  author = {Michael Lawrence and Vince Carey and Robert Gentleman},
  year = {2024},
  note = {R package version 1.66.0},
  url = {https://bioconductor.org/packages/rtracklayer},
  doi = {10.18129/B9.bioc.rtracklayer},
}

@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},
}

@Manual{R-UpSetR,
  title = {UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets},
  author = {Nils Gehlenborg},
  year = {2019},
  note = {R package version 1.4.0},
  url = {http://github.com/hms-dbmi/UpSetR},
}

@Manual{R-Vennerable,
  title = {Vennerable: Venn and Euler area-proportional diagrams},
  author = {Jonathan Swinton},
  year = {2024},
  note = {R package version 3.1.0.9000},
  url = {https://github.com/js229/Vennerable},
}

@Manual{R-XML,
  title = {XML: Tools for Parsing and Generating XML Within R and S-Plus},
  author = {Duncan {Temple Lang}},
  year = {2024},
  note = {R package version 3.99-0.17},
  url = {https://www.omegahat.net/RSXML/},
}

@Manual{R-XVector,
  title = {XVector: Foundation of external vector representation and manipulation in
Bioconductor},
  author = {Hervé Pagès and Patrick Aboyoun},
  year = {2024},
  note = {R package version 0.46.0},
  url = {https://bioconductor.org/packages/XVector},
  doi = {10.18129/B9.bioc.XVector},
}

@Article{airway2014,
  author = {{Himes} and B. E. and {Jiang} and {X.} and {Wagner} and {P.} and {Hu} and {R.} and {Wang} and {Q.} and {Klanderman} and {B.} and {Whitaker} and R. M. and {Duan} and {Q.} and {Lasky-Su} and {J.} and {Nikolos} and {C.} and {Jester} and {W.} and {Johnson} and {M.} and {Panettieri} and R. A. and {Tantisira} and K. G. and {Weiss} and S. T. and {Lu} and {Q.}},
  title = {{{R}{N}{A}-{S}eq {T}ranscriptome {P}rofiling {I}dentifies {C}{R}{I}{S}{P}{L}{D}2 as a {G}lucocorticoid {R}esponsive {G}ene that {M}odulates {C}ytokine {F}unction in {A}irway {S}mooth {M}uscle {C}ells}},
  journal = {PLoS ONE},
  year = {2014},
  volume = {9},
  number = {6},
  pages = {e99625},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/24926665},
}

@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},
}

@Book{class2002,
  title = {Modern Applied Statistics with S},
  author = {W. N. Venables and B. D. Ripley},
  publisher = {Springer},
  edition = {Fourth},
  address = {New York},
  year = {2002},
  note = {ISBN 0-387-95457-0},
  url = {https://www.stats.ox.ac.uk/pub/MASS4/},
}

@Article{ComplexHeatmap2016,
  title = {Complex heatmaps reveal patterns and correlations in multidimensional genomic data},
  author = {Zuguang Gu and Roland Eils and Matthias Schlesner},
  journal = {Bioinformatics},
  doi = {10.1093/bioinformatics/btw313},
  year = {2016},
}

@Article{ComplexHeatmap2022,
  title = {Complex Heatmap Visualization},
  author = {Zuguang Gu},
  doi = {10.1002/imt2.43},
  journal = {iMeta},
  year = {2022},
}

@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},
}

@Book{lattice2008,
  title = {Lattice: Multivariate Data Visualization with R},
  author = {Deepayan Sarkar},
  year = {2008},
  publisher = {Springer},
  address = {New York},
  isbn = {978-0-387-75968-5},
  url = {http://lmdvr.r-forge.r-project.org},
}

@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{MSnbase2012,
  title = {MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation},
  author = {Laurent Gatto and Kathryn Lilley},
  journal = {Bioinformatics},
  year = {2012},
  volume = {28},
  pages = {288-289},
}

@Article{MSnbase2020,
  title = {MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data},
  author = {Laurent Gatto and Sebastian Gibb and Johannes Rainer},
  journal = {bioRxiv},
  year = {2020},
}

@Article{MultiAssayExperiment2017,
  title = {Software For The Integration Of Multi-Omics Experiments In Bioconductor},
  author = {Marcel Ramos and Lucas Schiffer and Angela Re and Rimsha Azhar and Azfar Basunia and Carmen {Rodriguez Cabrera} and Tiffany Chan and Philip Chapman and Sean Davis and David Gomez-Cabrero and Aedin C. Culhane and Benjamin Haibe-Kains and Kasper Hansen and Hanish Kodali and Marie S Louis and Arvind S Mer and Markus Reister and Martin Morgan and Vincent J Carey and Levi Waldron},
  journal = {Cancer Research},
  year = {2017},
  volume = {77},
  number = {21},
  pages = {e39-42},
  doi = {10.1158/0008-5472.CAN-17-0344},
  url = {https://cancerres.aacrjournals.org/content/77/21/e39},
}

@Article{mzR2012,
  author = {{Chambers} and Matthew C. and {Maclean} and {Brendan} and {Burke} and {Robert} and {Amodei} and {Dario} and {Ruderman} and Daniel L. and {Neumann} and {Steffen} and {Gatto} and {Laurent} and {Fischer} and {Bernd} and {Pratt} and {Brian} and {Egertson} and {Jarrett} and {Hoff} and {Katherine} and {Kessner} and {Darren} and {Tasman} and {Natalie} and {Shulman} and {Nicholas} and {Frewen} and {Barbara} and {Baker} and Tahmina A. and {Brusniak} and {Mi-Youn} and {Paulse} and {Christopher} and {Creasy} and {David} and {Flashner} and {Lisa} and {Kani} and {Kian} and {Moulding} and {Chris} and {Seymour} and Sean L. and {Nuwaysir} and Lydia M. and {Lefebvre} and {Brent} and {Kuhlmann} and {Frank} and {Roark} and {Joe} and {Rainer} and {Paape} and {Detlev} and {Suckau} and {Hemenway} and {Tina} and {Huhmer} and {Andreas} and {Langridge} and {James} and {Connolly} and {Brian} and {Chadick} and {Trey} and {Holly} and {Krisztina} and {Eckels} and {Josh} and {Deutsch} and Eric W. and {Moritz} and Robert L. and {Katz} and Jonathan E. and {Agus} and David B. and {MacCoss} and {Michael} and {Tabb} and David L. and {Mallick} and {Parag}},
  year = {2012},
  journal = {Nat Biotech},
  title = {{A cross-platform toolkit for mass spectrometry and proteomics}},
  doi = {10.1038/nbt.2377},
  pmid = {23051804},
  month = {oct},
  number = {10},
  volume = {30},
  pages = {918--920},
  url = {http://dx.doi.org/10.1038/nbt.2377},
}

@Article{mzR2010,
  author = {Lennart Martens and Matthew Chambers and Marc Sturm and Darren Kessner and Fredrik Levander and Jim Shofstahl and Wilfred H Tang and Andreas Rompp and Steffen Neumann and Angel D Pizarro and Luisa Montecchi-Palazzi and Natalie Tasman and Mike Coleman and Florian Reisinger and Puneet Souda and Henning Hermjakob and Pierre-Alain Binz and Eric W Deutsch},
  title = {mz{ML} - a {C}ommunity {S}tandard for {M}ass {S}pectrometry {D}ata.},
  journal = {{Mol Cell Proteomics}},
  year = {2010},
  pmid = {20716697},
  doi = {10.1074/mcp.R110.000133},
}

@Article{mzR2004,
  author = {Patrick G A Pedrioli and Jimmy K Eng and Robert Hubley and Mathijs Vogelzang and Eric W Deutsch and Brian Raught and Brian Pratt and Erik Nilsson and Ruth H Angeletti and Rolf Apweiler and Kei Cheung and Catherine E Costello and Henning Hermjakob and Sequin Huang and Randall K Julian and Eugene Kapp and Mark E McComb and Stephen G Oliver and Gilbert Omenn and Norman W Paton and Richard Simpson and Richard Smith and Chris F Taylor and Weimin Zhu and Ruedi Aebersold},
  title = {{A} common open representation of mass spectrometry data and its
	application to proteomics research.},
  journal = {Nat Biotechnol},
  year = {2004},
  volume = {22},
  number = {11},
  pages = {{1459--1466}},
  pmid = {15529173},
  doi = {10.1038/nbt1031},
}

@Article{mzR2005,
  author = {Andrew Keller and Jimmy Eng and Ning Zhang and Xiao-jun Li and Ruedi Aebersold},
  title = {{A} uniform proteomics {MS}/{MS} analysis platform utilizing open {XML} file formats.},
  journal = {Mol Syst Biol},
  year = {2005},
}

@Article{mzR2008,
  author = {Darren Kessner and Matt Chambers and Robert Burke and David Agus and Parag Mallick},
  title = {{P}roteo{W}izard: open source software for rapid proteomics tools
	development.},
  journal = {Bioinformatics},
  year = {2008},
  volume = {24},
  number = {21},
  pages = {2534--2536},
  doi = {10.1093/bioinformatics/btn323},
  pmid = {18606607},
}

@Book{plotly2020,
  author = {Carson Sievert},
  title = {Interactive Web-Based Data Visualization with R, plotly, and shiny},
  publisher = {Chapman and Hall/CRC},
  year = {2020},
  isbn = {9781138331457},
  url = {https://plotly-r.com},
}

@Article{pRoloc2014a,
  title = {Mass-spectrometry based spatial proteomics data analysis using pRoloc and pRolocdata},
  author = {Laurent Gatto and Lisa M. Breckels and Samuel Wieczorek and Thomas Burger and Kathryn S. Lilley},
  journal = {Bioinformatics},
  year = {2014},
}

@Article{pRoloc2013a,
  title = {The effect of organelle discovery upon sub-cellular protein localisation},
  author = {Lisa M. Breckels and Laurent Gatto and Andy Christoforou and Arnoud J. Groen and Kathryn S. Lilley and Matthew W. Trotter},
  journal = {J Proteomics},
  year = {2013},
}

@Article{pRoloc2014b,
  title = {A foundation for reliable spatial proteomics data analysis},
  author = {Laurent Gatto and Lisa M. Breckels and Thomas Burger and Daniel J. Nightingale and Arnoud J. Groen and Callum Campbell and Claire M. Mulvey and Andy Christroforou and Myriam Ferro and Kathryn S. Lilley},
  journal = {Mol Cell Proteomics},
  year = {2014},
}

@Article{pRoloc2016a,
  title = {Learning from heterogeneous data sources: an application in spatial proteomics},
  author = {Lisa M. Breckels and Sean Holden and David Wonjar and Claire M. Mulvey and Andy Christoforou and Arnoud Groen and Matthew W.B. Trotter and Oliver Kohlbacker and Kathryn S. Lilley and Laurent Gatto},
  journal = {PLoS Comput Biol},
  year = {2016},
}

@Article{pRoloc2016b,
  title = {A Bioconductor workflow for processing and analysing spatial proteomics data},
  author = {Lisa M. Breckels and Claire M. Mulvey and Kathryn S. Lilley and Laurent Gatto},
  journal = {F1000Research},
  year = {2016},
}

@Article{pRoloc2019a,
  title = {A Bioconductor workflow for the Bayesian analysis of spatial proteomics},
  author = {Oliver M. Crook and Lisa M. Breckels and Kathryn S. Lilley and Paul D.W. Kirk and Laurent Gatto},
  journal = {F1000Research},
  year = {2019},
}

@Article{Rcpp2011,
  title = {{Rcpp}: Seamless {R} and {C++} Integration},
  author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {40},
  number = {8},
  pages = {1--18},
  doi = {10.18637/jss.v040.i08},
}

@Book{Rcpp2013,
  title = {Seamless {R} and {C++} Integration with {Rcpp}},
  author = {Dirk Eddelbuettel},
  publisher = {Springer},
  address = {New York},
  year = {2013},
  note = {ISBN 978-1-4614-6867-7},
  doi = {10.1007/978-1-4614-6868-4},
}

@Article{Rcpp2018,
  title = {{Extending {R} with {C++}: A Brief Introduction to {Rcpp}}},
  author = {Dirk Eddelbuettel and James Joseph Balamuta},
  journal = {The American Statistician},
  year = {2018},
  volume = {72},
  number = {1},
  pages = {28-36},
  doi = {10.1080/00031305.2017.1375990},
}

@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{rtracklayer2009,
  title = {rtracklayer: an R package for interfacing with
                  genome browsers},
  author = {Michael Lawrence and Robert Gentleman and Vincent Carey},
  year = {2009},
  journal = {Bioinformatics},
  volume = {25},
  pages = {1841-1842},
  doi = {10.1093/bioinformatics/btp328},
  url = {http://bioinformatics.oxfordjournals.org/content/25/14/1841.abstract},
}

@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},
}