r-packages.bib

@Manual{R-biomaRt,
  title = {biomaRt: Interface to BioMart databases (i.e. Ensembl)},
  author = {Steffen Durinck and Wolfgang Huber},
  year = {2022},
  note = {R package version 2.52.0},
}

@Manual{R-Biostrings,
  title = {Biostrings: Efficient manipulation of biological strings},
  author = {H. Pagès and P. Aboyoun and R. Gentleman and S. DebRoy},
  year = {2022},
  note = {R package version 2.64.0},
  url = {https://bioconductor.org/packages/Biostrings},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2022},
  note = {R package version 0.26},
  url = {https://CRAN.R-project.org/package=bookdown},
}

@Manual{R-circlize,
  title = {circlize: Circular Visualization},
  author = {Zuguang Gu},
  year = {2022},
  note = {R package version 0.4.14},
  url = {https://CRAN.R-project.org/package=circlize},
}

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

@Manual{R-ComplexHeatmap,
  title = {ComplexHeatmap: Make Complex Heatmaps},
  author = {Zuguang Gu},
  year = {2022},
  note = {https://github.com/jokergoo/ComplexHeatmap},
}

@Manual{R-downlit,
  title = {downlit: Syntax Highlighting and Automatic Linking},
  author = {Hadley Wickham},
  year = {2021},
  note = {R package version 0.4.0},
  url = {https://CRAN.R-project.org/package=downlit},
}

@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
  year = {2022},
  note = {R package version 1.0.9},
  url = {https://CRAN.R-project.org/package=dplyr},
}

@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 = {2022},
  note = {R package version 3.3.6},
  url = {https://CRAN.R-project.org/package=ggplot2},
}

@Manual{R-GOSemSim,
  title = {GOSemSim: GO-terms Semantic Similarity Measures},
  author = {Guangchuang Yu},
  year = {2022},
  note = {R package version 2.22.0},
  url = {https://yulab-smu.top/biomedical-knowledge-mining-book/},
}

@Manual{R-GOstats,
  title = {GOstats: Tools for manipulating GO and microarrays},
  author = {Robert Gentleman},
  year = {2022},
  note = {R package version 2.62.0},
}

@Manual{R-kableExtra,
  title = {kableExtra: Construct Complex Table with kable and Pipe Syntax},
  author = {Hao Zhu},
  year = {2021},
  note = {R package version 1.3.4},
  url = {https://CRAN.R-project.org/package=kableExtra},
}

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2022},
  note = {R package version 1.39},
  url = {https://yihui.org/knitr/},
}

@Manual{R-limma,
  title = {limma: Linear Models for Microarray Data},
  author = {Gordon Smyth and Yifang Hu and Matthew Ritchie and Jeremy Silver and James Wettenhall and Davis McCarthy and Di Wu and Wei Shi and Belinda Phipson and Aaron Lun and Natalie Thorne and Alicia Oshlack and Carolyn {de Graaf} and Yunshun Chen and Mette Langaas and Egil Ferkingstad and Marcus Davy and Francois Pepin and Dongseok Choi},
  year = {2022},
  note = {R package version 3.52.0},
  url = {http://bioinf.wehi.edu.au/limma},
}

@Manual{R-MSnID,
  title = {MSnID: Utilities for Exploration and Assessment of Confidence of LC-MSn
Proteomics Identifications},
  author = {Vladislav Petyuk},
  year = {2022},
  note = {R package version 1.25.1},
}

@Manual{R-MSnSet.utils,
  title = {MSnSet.utils: Miscellaneous Functions for Proteomics Data Analysis},
  author = {Vladislav Petyuk},
  year = {2021},
  note = {R package version 0.1},
}

@Manual{R-org.Hs.eg.db,
  title = {org.Hs.eg.db: Genome wide annotation for Human},
  author = {Marc Carlson},
  year = {2022},
  note = {R package version 3.15.0},
}

@Manual{R-PlexedPiper,
  title = {PlexedPiper: Pipeline for isobaric quantification},
  author = {Vladislav Petyuk vladislav.petyuk@pnnl.gov},
  year = {2022},
  note = {R package version 0.3.5},
}

@Manual{R-PlexedPiperTestData,
  title = {PlexedPiperTestData: Example of MASIC and MS-GF+ ouput},
  author = {Vladislav Petyuk},
  year = {2022},
  note = {R package version 0.1.0},
}

@Manual{R-PNNL.DMS.utils,
  title = {PNNL.DMS.utils: Tools for accessing PNNL's Data Management System},
  author = {Vladislav Petyuk and Michael Nestor and Jamie Moon},
  year = {2022},
  note = {R package version 0.1.8},
}

@Manual{R-ReactomePA,
  title = {ReactomePA: Reactome Pathway Analysis},
  author = {Guangchuang Yu},
  year = {2022},
  note = {R package version 1.40.0},
  url = {https://yulab-smu.top/biomedical-knowledge-mining-book/},
}

@Manual{R-rmarkdown,
  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 = {2022},
  note = {R package version 2.14},
  url = {https://CRAN.R-project.org/package=rmarkdown},
}

@Manual{R-scales,
  title = {scales: Scale Functions for Visualization},
  author = {Hadley Wickham and Dana Seidel},
  year = {2022},
  note = {R package version 1.2.0},
  url = {https://CRAN.R-project.org/package=scales},
}

@Manual{R-tibble,
  title = {tibble: Simple Data Frames},
  author = {Kirill Müller and Hadley Wickham},
  year = {2021},
  note = {R package version 3.1.6},
  url = {https://CRAN.R-project.org/package=tibble},
}

@Manual{R-writexl,
  title = {writexl: Export Data Frames to Excel xlsx Format},
  author = {Jeroen Ooms},
  year = {2021},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=writexl},
}

@Article{biomaRt2009,
  title = {Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt},
  author = {Steffen Durinck and Paul T. Spellman and Ewan Birney and Wolfgang Huber},
  journal = {Nature Protocols},
  year = {2009},
  volume = {4},
  pages = {1184--1191},
}

@Article{biomaRt2005,
  title = {BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis},
  author = {Steffen Durinck and Yves Moreau and Arek Kasprzyk and Sean Davis and Bart {De Moor} and Alvis Brazma and Wolfgang Huber},
  journal = {Bioinformatics},
  year = {2005},
  volume = {21},
  pages = {3439--3440},
}

@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},
  note = {ISBN 978-1138700109},
  url = {https://bookdown.org/yihui/bookdown},
}

@Article{circlize2014,
  title = {circlize implements and enhances circular visualization in R},
  author = {Zuguang Gu and Lei Gu and Roland Eils and Matthias Schlesner and Benedikt Brors},
  journal = {Bioinformatics},
  volume = {30},
  issue = {19},
  pages = {2811-2812},
  year = {2014},
}

@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},
}

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

@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{GOSemSim2020,
  title = {Gene Ontology Semantic Similarity Analysis Using GOSemSim},
  author = {Guangchuang Yu},
  journal = {Methods in Molecular Biology},
  shortjournal = {Methods Mol. Biol.},
  year = {2020},
  volume = {2117},
  pages = {207-215},
  pmid = {31960380},
  issn = {1940-6029},
  doi = {10.1007/978-1-0716-0301-7_11},
}

@Article{GOSemSim2010,
  title = {GOSemSim: an R package for measuring semantic similarity among GO terms and gene products},
  author = {Guangchuang Yu and Fei Li and Yide Qin and Xiaochen Bo and Yibo Wu and Shengqi Wang},
  journal = {Bioinformatics},
  year = {2010},
  volume = {26},
  number = {7},
  pages = {976-978},
  pmid = {20179076},
  doi = {10.1093/bioinformatics/btq064},
}

@Article{GOstats2007,
  author = {S Falcon and R Gentleman},
  title = {Using {G}{O}stats to test gene lists for {G}{O} term association.},
  journal = {Bioinformatics},
  year = {2007},
  volume = {23},
  number = {2},
  pages = {257-8},
}

@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},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}

@Article{limma2015,
  author = {Matthew E Ritchie and Belinda Phipson and Di Wu and Yifang Hu and Charity W Law and Wei Shi and Gordon K Smyth},
  title = {{limma} powers differential expression analyses for {RNA}-sequencing and microarray studies},
  journal = {Nucleic Acids Research},
  year = {2015},
  volume = {43},
  number = {7},
  pages = {e47},
  doi = {10.1093/nar/gkv007},
}

@Article{ReactomePA2016,
  title = {ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization},
  author = {Guangchuang Yu and Qing-Yu He},
  journal = {Molecular BioSystems},
  year = {2016},
  volume = {12},
  number = {12},
  pages = {477-479},
  pmid = {26661513},
  url = {http://pubs.rsc.org/en/Content/ArticleLanding/2015/MB/C5MB00663E},
  doi = {10.1039/C5MB00663E},
}

@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},
  note = {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},
  note = {ISBN 9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}