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 = {2018},
  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 = {2017},
  note = {R package version 2.38.0},
}
@Manual{R-BiocGenerics,
  title = {BiocGenerics: S4 generic functions for Bioconductor},
  author = {The Bioconductor Dev Team},
  year = {2017},
  note = {R package version 0.24.0},
}
@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2019},
  note = {R package version 0.14},
  url = {https://CRAN.R-project.org/package=bookdown},
}
@Manual{R-DelayedArray,
  title = {DelayedArray: Delayed operations on array-like objects},
  author = {Hervé Pagès},
  year = {2017},
  note = {R package version 0.4.1},
}
@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 = {2017},
  note = {R package version 1.18.1},
  url = {https://github.com/mikelove/DESeq2},
}
@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
  year = {2019},
  note = {R package version 0.8.3},
  url = {https://CRAN.R-project.org/package=dplyr},
}
@Manual{R-forcats,
  title = {forcats: Tools for Working with Categorical Variables (Factors)},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 0.4.0},
  url = {https://CRAN.R-project.org/package=forcats},
}
@Manual{R-fs,
  title = {fs: Cross-Platform File System Operations Based on 'libuv'},
  author = {Jim Hester and Hadley Wickham},
  year = {2019},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=fs},
}
@Manual{R-GenomeInfoDb,
  title = {GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname'
identifiers},
  author = {Sonali Arora and Martin Morgan and Marc Carlson and H. Pagès},
  year = {2017},
  note = {R package version 1.14.0},
}
@Manual{R-GenomicRanges,
  title = {GenomicRanges: Representation and manipulation of genomic intervals and
variables defined along a genome},
  author = {P. Aboyoun and H. Pagès and M. Lawrence},
  year = {2018},
  note = {R package version 1.30.3},
}
@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},
  year = {2019},
  note = {R package version 3.2.1},
  url = {https://CRAN.R-project.org/package=ggplot2},
}
@Manual{R-here,
  title = {here: A Simpler Way to Find Your Files},
  author = {Kirill Müller},
  year = {2017},
  note = {R package version 0.1},
  url = {https://CRAN.R-project.org/package=here},
}
@Manual{R-IRanges,
  title = {IRanges: Infrastructure for manipulating intervals on sequences},
  author = {H. Pagès and P. Aboyoun and M. Lawrence},
  year = {2017},
  note = {R package version 2.12.0},
}
@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2019},
  note = {R package version 1.25},
  url = {https://CRAN.R-project.org/package=knitr},
}
@Manual{R-matrixStats,
  title = {matrixStats: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)},
  author = {Henrik Bengtsson},
  year = {2019},
  note = {R package version 0.55.0},
  url = {https://CRAN.R-project.org/package=matrixStats},
}
@Manual{R-purrr,
  title = {purrr: Functional Programming Tools},
  author = {Lionel Henry and Hadley Wickham},
  year = {2019},
  note = {R package version 0.3.3},
  url = {https://CRAN.R-project.org/package=purrr},
}
@Manual{R-readr,
  title = {readr: Read Rectangular Text Data},
  author = {Hadley Wickham and Jim Hester and Romain Francois},
  year = {2018},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=readr},
}
@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 = {2019},
  note = {R package version 1.16},
  url = {https://CRAN.R-project.org/package=rmarkdown},
}
@Manual{R-Rtsne,
  title = {Rtsne: T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
Implementation},
  author = {Jesse Krijthe},
  year = {2018},
  note = {R package version 0.15},
  url = {https://CRAN.R-project.org/package=Rtsne},
}
@Manual{R-S4Vectors,
  title = {S4Vectors: S4 implementation of vector-like and list-like objects},
  author = {H. Pagès and M. Lawrence and P. Aboyoun},
  year = {2017},
  note = {R package version 0.16.0},
}
@Manual{R-shiny,
  title = {shiny: Web Application Framework for R},
  author = {Winston Chang and Joe Cheng and JJ Allaire and Yihui Xie and Jonathan McPherson},
  year = {2019},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=shiny},
}
@Manual{R-stringr,
  title = {stringr: Simple, Consistent Wrappers for Common String Operations},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=stringr},
}
@Manual{R-SummarizedExperiment,
  title = {SummarizedExperiment: SummarizedExperiment container},
  author = {Martin Morgan and Valerie Obenchain and Jim Hester and Hervé Pagès},
  year = {2017},
  note = {R package version 1.8.1},
}
@Manual{R-tibble,
  title = {tibble: Simple Data Frames},
  author = {Kirill Müller and Hadley Wickham},
  year = {2019},
  note = {R package version 2.1.3},
  url = {https://CRAN.R-project.org/package=tibble},
}
@Manual{R-tidyr,
  title = {tidyr: Tidy Messy Data},
  author = {Hadley Wickham and Lionel Henry},
  year = {2019},
  note = {R package version 1.0.0},
  url = {https://CRAN.R-project.org/package=tidyr},
}
@Manual{R-tidyverse,
  title = {tidyverse: Easily Install and Load the 'Tidyverse'},
  author = {Hadley Wickham},
  year = {2017},
  note = {R package version 1.2.1},
  url = {https://CRAN.R-project.org/package=tidyverse},
}