references.bib

@Manual{SE,
    title = {SummarizedExperiment: SummarizedExperiment container},
    author = {Martin Morgan and Valerie Obenchain and Jim Hester and Hervé Pagès},
    year = {2020},
    note = {R package version 1.20.0},
    url = {https://bioconductor.org/packages/SummarizedExperiment},
  }

@Article{SCE,
    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},
  }

@Manual{TSE,
    title = {TreeSummarizedExperiment: TreeSummarizedExperiment: a S4 Class for Data with Tree
Structures},
    author = {Ruizhu Huang},
    year = {2021},
    note = {R package version 1.99.9},
  }

@Article{dada2,
    title = {DADA2: High-resolution sample inference from Illumina amplicon data},
    author = {Benjamin J Callahan and Paul J McMurdie and Michael J Rosen and Andrew W Han and Amy Jo A Johnson and Susan P Holmes},
    journal = {Nature Methods},
    volume = {13},
    pages = {581-583},
    year = {2016},
    doi = {10.1038/nmeth.3869},
  }

 @Manual{DMM,
    title = {DirichletMultinomial: Dirichlet-Multinomial Mixture Model Machine Learning for
Microbiome Data},
    author = {Martin Morgan},
    year = {2020},
    note = {R package version 1.32.0},
  }