@Manual{core2024r,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2024},
  url = {https://www.R-project.org/},
  }

@misc{benedetti2024iseetree,
  title={iSEEtree: interactive explorer for hierarchical data}, 
  author={Giulio Benedetti and Ely Seraidarian and Theotime Pralas and Akewak Jeba and Tuomas Borman and Leo Lahti},
  year={2024},
  eprint={2412.02882},
  archivePrefix={arXiv},
  primaryClass={cs.MS},
  url={https://arxiv.org/abs/2412.02882}
}

@article{rue2018isee,
  title={iSEE: interactive summarizedexperiment explorer},
  author={Rue-Albrecht, Kevin and Marini, Federico and Soneson, Charlotte and Lun, Aaron TL},
  journal={F1000Research},
  volume={7},
  year={2018},
  publisher={Faculty of 1000 Ltd},
  doi={10.12688/f1000research.14966.1}
}

@Manual{chang2024shiny,
    title = {shiny: Web Application Framework for R},
    author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
    year = {2024},
    note = {R package version 1.9.1},
    url = {https://CRAN.R-project.org/package=shiny},
  }

@Manual{borman2024mia,
  title = {mia: Microbiome analysis},
  author = {Tuomas Borman and Felix G.M. Ernst and Sudarshan A. Shetty and Leo Lahti},
  year = {2024},
  note = {R package version 1.14.0},
  url = {https://bioconductor.org/packages/mia},
  doi = {10.18129/B9.bioc.mia},
}

@article{huang2020treesummarizedexperiment,
  title={TreeSummarizedExperiment: a S4 class for data with hierarchical structure},
  author={Huang, Ruizhu and Soneson, Charlotte and Ernst, Felix GM and Rue-Albrecht, Kevin C and Yu, Guangchuang and Hicks, Stephanie C and Robinson, Mark D},
  journal={F1000Research},
  volume={9},
  year={2020},
  publisher={Faculty of 1000 Ltd},
  doi={10.12688/f1000research.26669.2}
}