packages.bib

@misc{Soneson2024,
  title =	 {{Learning and teaching biological data science in
                  the Bioconductor community}},
  author =	 {Jenny Drnevich and Frederick J. Tan and Fabricio
                  Almeida-Silva and Robert Castelo and Aedin
                  C. Culhane and Sean Davis and Maria A. Doyle and
                  Susan Holmes and Leo Lahti and Alexandru Mahmoud and
                  Kozo Nishida and Marcel Ramos and Kevin Rue-Albrecht
                  and David J. H. Shih and Laurent Gatto and Charlotte
                  Soneson},
  year =	 2024,
  eprint =	 {2410.01351},
  archivePrefix ={arXiv},
  primaryClass = {cs.CY},
  url =		 {https://arxiv.org/abs/2410.01351},
}

@Manual{miacourse,
  title =	 {Multi-omic data science with R/Bioconductor},
  author =	 {{Tuomas Borman} and {Leo Lahti}},
  year =	 2024,
  url =		 {microbiome.github.io}
}

@Manual{oulu2023course,
  title =	 {Multi-omic data science with R/Bioconductor. Oulu
                  Summer School.},
  author =	 {Tuomas Borman and Anna Kaisanlahti and Justus Reunanen
                  and Leo Lahti},
  year =	 2024,
  url =		 {microbiome.github.io/course_2024_oulu}
}

@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},
}

@Article{ijerph18084049,
AUTHOR = {Hintikka, Jukka and Lensu, Sanna and Mäkinen, Elina and Karvinen, Sira and Honkanen, Marjaana and Lindén, Jere and Garrels, Tim and Pekkala, Satu and Lahti, Leo},
TITLE = {Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering},
JOURNAL = {International Journal of Environmental Research and Public Health},
VOLUME = {18},
YEAR = {2021},
NUMBER = {8},
ARTICLE-NUMBER = {4049},
URL = {https://www.mdpi.com/1660-4601/18/8/4049},
PubMedID = {33921370},
ISSN = {1660-4601},
DOI = {10.3390/ijerph18084049}
}