packages.bib

@Manual{radboud2021course,
  title = {Introduction to microbiome data science with miaverse. Radboud Summer School.},
  author = {Tuomas Borman and Henrik Eckermann and Chouaib Benchraka and Leo Lahti},
  year = {2021},
  url = {microbiome.github.io/course_2021_radboud/}
}


@Manual{R-ANCOMBC,
  title = {ANCOMBC: Analysis of compositions of microbiomes with bias correction},
  author = {Huang Lin and Shyamal Das Peddada},
  year = {2021},
  note = {R package version 1.2.0},
  url = {https://github.com/FrederickHuangLin/ANCOMBC},
}

@Manual{R-ape,
  title = {ape: Analyses of Phylogenetics and Evolution},
  author = {Emmanuel Paradis and Simon Blomberg and Ben Bolker and Joseph Brown and Santiago Claramunt and Julien Claude and Hoa Sien Cuong and Richard Desper and Gilles Didier and Benoit Durand and Julien Dutheil and RJ Ewing and Olivier Gascuel and Thomas Guillerme and Christoph Heibl and Anthony Ives and Bradley Jones and Franz Krah and Daniel Lawson and Vincent Lefort and Pierre Legendre and Jim Lemon and Guillaume Louvel and Eric Marcon and Rosemary McCloskey and Johan Nylander and Rainer Opgen-Rhein and Andrei-Alin Popescu and Manuela Royer-Carenzi and Klaus Schliep and Korbinian Strimmer and Damien {de Vienne}},
  year = {2021},
  note = {R package version 5.5},
  url = {http://ape-package.ird.fr/},
}

@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 = {2021},
  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 = {2021},
  note = {R package version 2.52.0},
  url = {https://bioconductor.org/packages/Biobase},
}

@Manual{R-BiocGenerics,
  title = {BiocGenerics: S4 generic functions used in Bioconductor},
  author = {The Bioconductor Dev Team},
  year = {2021},
  note = {R package version 0.38.0},
  url = {https://bioconductor.org/packages/BiocGenerics},
}

@Manual{R-BiocManager,
  title = {BiocManager: Access the Bioconductor Project Package Repository},
  author = {Martin Morgan},
  year = {2021},
  note = {R package version 1.30.16},
  url = {https://CRAN.R-project.org/package=BiocManager},
}

@Manual{R-Biostrings,
  title = {Biostrings: Efficient manipulation of biological strings},
  author = {H. Pagès and P. Aboyoun and R. Gentleman and S. DebRoy},
  year = {2021},
  note = {R package version 2.60.1},
  url = {https://bioconductor.org/packages/Biostrings},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2021},
  note = {R package version 0.22},
  url = {https://CRAN.R-project.org/package=bookdown},
}

@Manual{R-DESeq2,
  title = {DESeq2: Differential gene expression analysis based on the negative
binomial distribution},
  author = {Michael Love and Simon Anders and Wolfgang Huber},
  year = {2021},
  note = {R package version 1.32.0},
  url = {https://github.com/mikelove/DESeq2},
}

@Manual{R-DirichletMultinomial,
  title = {DirichletMultinomial: Dirichlet-Multinomial Mixture Model Machine Learning for
Microbiome Data},
  author = {Martin Morgan},
  year = {2021},
  note = {R package version 1.34.0},
}

@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
  year = {2021},
  note = {R package version 1.0.7},
  url = {https://CRAN.R-project.org/package=dplyr},
}

@Manual{R-ecodist,
  title = {ecodist: Dissimilarity-Based Functions for Ecological Analysis},
  author = {Sarah Goslee and Dean Urban},
  year = {2020},
  note = {R package version 2.0.7},
  url = {https://CRAN.R-project.org/package=ecodist},
}

@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 H. Pagès},
  year = {2021},
  note = {R package version 1.28.0},
  url = {https://bioconductor.org/packages/GenomeInfoDb},
}

@Manual{R-GenomicRanges,
  title = {GenomicRanges: Representation and manipulation of genomic intervals},
  author = {P. Aboyoun and H. Pagès and M. Lawrence},
  year = {2021},
  note = {R package version 1.44.0},
  url = {https://bioconductor.org/packages/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},
  year = {2021},
  note = {R package version 3.3.5},
  url = {https://CRAN.R-project.org/package=ggplot2},
}

@Manual{R-ggraph,
  title = {ggraph: An Implementation of Grammar of Graphics for Graphs and Networks},
  author = {Thomas Lin Pedersen},
  year = {2021},
  note = {R package version 2.0.5},
  url = {https://CRAN.R-project.org/package=ggraph},
}

@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-IRanges,
  title = {IRanges: Foundation of integer range manipulation in Bioconductor},
  author = {H. Pagès and P. Aboyoun and M. Lawrence},
  year = {2021},
  note = {R package version 2.26.0},
  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 = {2021},
  note = {R package version 1.33},
  url = {https://yihui.org/knitr/},
}

@Manual{R-lattice,
  title = {lattice: Trellis Graphics for R},
  author = {Deepayan Sarkar},
  year = {2021},
  note = {R package version 0.20-44},
  url = {http://lattice.r-forge.r-project.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 = {2021},
  note = {R package version 1.4.0},
  url = {https://bioconductor.org/packages/MatrixGenerics},
}

@Manual{R-matrixStats,
  title = {matrixStats: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)},
  author = {Henrik Bengtsson},
  year = {2021},
  note = {R package version 0.59.0},
  url = {https://github.com/HenrikBengtsson/matrixStats},
}

@Manual{R-mia,
  title = {mia: Microbiome analysis},
  author = {Felix G.M. Ernst and Sudarshan A. Shetty and Tuomas Borman and Leo Lahti},
  year = {2021},
  note = {R package version 1.0.5},
  url = {https://github.com/microbiome/mia},
}

@Manual{R-miaViz,
  title = {miaViz: Microbiome Analysis Plotting and Visualization},
  author = {Felix G.M. Ernst and Tuomas Borman},
  year = {2021},
  note = {R package version 1.0.1},
}

@Manual{R-permute,
  title = {permute: Functions for Generating Restricted Permutations of Data},
  author = {Gavin L. Simpson},
  year = {2019},
  note = {R package version 0.9-5},
  url = {https://github.com/gavinsimpson/permute},
}

@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 = {2021},
  note = {R package version 0.30.0},
  url = {https://bioconductor.org/packages/S4Vectors},
}

@Manual{R-SingleCellExperiment,
  title = {SingleCellExperiment: S4 Classes for Single Cell Data},
  author = {Aaron Lun and Davide Risso},
  year = {2021},
  note = {R package version 1.14.1},
}

@Manual{R-SummarizedExperiment,
  title = {SummarizedExperiment: SummarizedExperiment container},
  author = {Martin Morgan and Valerie Obenchain and Jim Hester and Hervé Pagès},
  year = {2021},
  note = {R package version 1.22.0},
  url = {https://bioconductor.org/packages/SummarizedExperiment},
}

@Manual{R-TreeSummarizedExperiment,
  title = {TreeSummarizedExperiment: a S4 Class for Data with Tree
Structures},
  author = {Ruizhu Huang},
  year = {2021},
  note = {R package version 2.0.2},
}

@Manual{R-vegan,
  title = {vegan: Community Ecology Package},
  author = {Jari Oksanen and F. Guillaume Blanchet and Michael Friendly and Roeland Kindt and Pierre Legendre and Dan McGlinn and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner},
  year = {2020},
  note = {R package version 2.5-7},
  url = {https://CRAN.R-project.org/package=vegan},
}

@Manual{R-XVector,
  title = {XVector: Foundation of external vector representation and manipulation in
Bioconductor},
  author = {Hervé Pagès and Patrick Aboyoun},
  year = {2021},
  note = {R package version 0.32.0},
  url = {https://bioconductor.org/packages/XVector},
}

@Article{ANCOMBC2020,
  title = {Analysis of compositions of microbiomes with bias correction},
  author = {Huang Lin and Shyamal Das Peddada},
  year = {2020},
  journal = {Nature communications},
  volume = {11},
  number = {1},
  pages = {1--11},
  doi = {https://doi.org/10.1038/s41467-020-17041-7},
  url = {https://www.nature.com/articles/s41467-020-17041-7},
}

@Article{ape2019,
  title = {ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}},
  author = {E. Paradis and K. Schliep},
  journal = {Bioinformatics},
  year = {2019},
  volume = {35},
  pages = {526-528},
}

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

@Article{DESeq22014,
  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},
}

@Article{ecodist2007,
  title = {The ecodist package for dissimilarity-based analysis of ecological data},
  author = {Sarah C. Goslee and Dean L. Urban},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {22},
  issue = {7},
  pages = {1-19},
}

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

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

@Article{SingleCellExperiment2020,
  title = {Orchestrating single-cell analysis with Bioconductor},
  author = {Robert Amezquita and Aaron Lun and Etienne Becht and Vince Carey and Lindsay Carpp and Ludwig Geistlinger and Federico Marini and Kevin Rue-Albrecht and Davide Risso and Charlotte Soneson and Levi Waldron and Herve Pages and Mike Smith and Wolfgang Huber and Martin Morgan and Raphael Gottardo and Stephanie Hicks},
  year = {2020},
  volume = {17},
  pages = {137--145},
  journal = {Nature Methods},
  url = {https://www.nature.com/articles/s41592-019-0654-x},
}

@Article{TreeSummarizedExperiment2021,
  title = {TreeSummarizedExperiment: a S4 class for data with hierarchical structure},
  author = {Ruizhu Huang and Charlotte Soneson and Felix G.M. Ernst and Kevin C. Rue-Albrecht and Guangchuang Yu and Stephanie C. Hicks and Mark D. Robinson},
  journal = {F1000Research},
  year = {2021},
  volume = {9},
  pages = {1246},
  url = {https://f1000research.com/articles/9-1246},
}