@Manual{R-cowplot,
  title = {{cowplot}: Streamlined Plot Theme and Plot
    Annotations for '{ggplot2}'},
  author = {Claus O. Wilke},
  year = {2019},
  note = {R package version 1.0.0},
  url = {https://CRAN.R-project.org/package=cowplot},
}

@Manual{R-dplyr,
  title = {{dplyr}: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel
    Henry and Kirill Müller},
  year = {2020},
  note = {R package version 1.0.1},
  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 = {2020},
  note = {R package version 3.3.2},
  url = {https://CRAN.R-project.org/package=ggplot2},
}

@Manual{R-ggtext,
  title = {{ggtext}: Improved Text Rendering Support for '{ggplot2}'},
  author = {Claus O. Wilke},
  year = {2020},
  note = {R package version 0.1.0},
  url = {https://CRAN.R-project.org/package=ggtext},
}

@Manual{R-magrittr,
  title = {{magrittr}: A Forward-Pipe Operator for R},
  author = {Stefan Milton Bache and Hadley Wickham},
  year = {2014},
  note = {R package version 1.5},
  url = {https://CRAN.R-project.org/package=magrittr},
}

@Manual{R-Seurat,
  title = {{Seurat}: Tools for Single Cell Genomics},
  author = {Rahul Satija and Andrew Butler and Paul Hoffman
    and Tim Stuart},
  year = {2020},
  note = {R package version 3.2.0},
  url = {https://CRAN.R-project.org/package=Seurat},
}

@Manual{R-SingleCellExperiment,
  title = {{SingleCellExperiment}: S4 Classes for Single Cell
    Data},
  author = {Aaron Lun and Davide Risso},
  year = {2020},
  note = {R package version 1.11.6},
}

@Manual{R-SummarizedExperiment,
  title = {{SummarizedExperiment}: SummarizedExperiment container},
  author = {Martin Morgan and Valerie Obenchain and Jim Hester
    and Hervé Pagès},
  year = {2020},
  note = {R package version 1.19.6},
}

@Manual{R-pheatmap,
  title = {{pheatmap}: Pretty Heatmaps},
  author = {Raivo Kolde},
  year = {2019},
  note = {R package version 1.0.12},
  url = {https://CRAN.R-project.org/package=pheatmap},
}

@Manual{R-RColorBrewer,
  title = {{RColorBrewer}: ColorBrewer Palettes},
  author = {Erich Neuwirth},
  year = {2014},
  note = {R package version 1.1-2},
  url = {https://CRAN.R-project.org/package=RColorBrewer},
}

@Manual{R-viridis,
  title = {{viridis}: Default Color Maps from 'matplotlib'},
  author = {Simon Garnier},
  year = {2018},
  note = {R package version 0.5.1},
  url = {https://CRAN.R-project.org/package=viridis},
}

@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{Seurat2019,
  author = {Tim Stuart and Andrew Butler and Paul Hoffman
    and Christoph Hafemeister and Efthymia Papalexi and William
    M Mauck III and Yuhan Hao and Marlon Stoeckius and Peter
    Smibert and Rahul Satija},
  title = {Comprehensive Integration of Single-Cell Data},
  journal = {Cell},
  year = {2019},
  volume = {177},
  pages = {1888-1902},
  doi = {10.1016/j.cell.2019.05.031},
  url = {https://doi.org/10.1016/j.cell.2019.05.031},
}

@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{DESeq2,
    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},
  }

