Please cite the microbiome package and related work as follows:

Shetty SA, Lahti L (2019). “Microbiome data science.” Journal of Biosciences, 44(5), 115. doi:10.1007/s12038-019-9930-2.

Borman T, Benedetti G, Muluh G, Raulo A, Valderrama B, Sannikov A, Peschel S, Liu Y, Hindström R, OMA consortium, Pärnänen K, Müller CL, Havulinna AS, Shetty S, Ramos M, Braccia DJ, Bravo H, Ernst FM, Waldron L, Bastiaanssen TFS, Mallick H, Lahti L (2025). “Orchestrating Microbiome Analysis with Bioconductor.” bioRxiv. doi:10.1101/2025.10.29.685036. Preprint.

Corresponding BibTeX entries:

  @Article{,
    title = {Microbiome data science},
    author = {Sudarshan A. Shetty and Leo Lahti},
    journal = {Journal of Biosciences},
    year = {2019},
    volume = {44},
    number = {5},
    pages = {115},
    doi = {10.1007/s12038-019-9930-2},
  }

  @Article{,
    title = {Orchestrating Microbiome Analysis with Bioconductor},
    author = {Tuomas Borman and Giulio Benedetti and Geraldson Muluh
      and Aura Raulo and Benjamin Valderrama and Artur Sannikov and
      Stefanie Peschel and Yihan Liu and Rasmus Hindström and {OMA
      consortium} and Katariina Pärnänen and Christian L. Müller and
      Aki S. Havulinna and Sudarshan Shetty and Marcel Ramos and
      Domenick J. Braccia and Héctor Corrada Bravo and Felix M. Ernst
      and Levi Waldron and Thomaz F. S. Bastiaanssen and Himel Mallick
      and Leo Lahti},
    journal = {bioRxiv},
    year = {2025},
    doi = {10.1101/2025.10.29.685036},
    note = {Preprint},
  }