To cite the original statistical method and normalization method implemented in metagenomeSeq use

Paulson JN, Stine OC, Bravo HC, Pop M (2013). “Differential abundance analysis for microbial marker-gene surveys.” Nat Meth, advance online publication. doi:10.1038/nmeth.2658. http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2658.html.

To cite the metagenomeSeq software/vignette guide use

Paulson JN, Olson ND, Braccia DJ, Wagner J, Talukder H, Pop M, Bravo HC (2013). metagenomeSeq: Statistical analysis for sparse high-throughput sequncing.. Bioconductor package, http://www.cbcb.umd.edu/software/metagenomeSeq.

To cite time series analysis/function fitTimeSeries use

Paulson* JN, Talukder* H, Bravo HC (2017). “Longitudinal differential abundance analysis of marker-gene surveys using smoothing splines.” biorxiv. doi:10.1101/099457. https://www.biorxiv.org/content/10.1101/099457v1.

Corresponding BibTeX entries:

  @Article{,
    title = {Differential abundance analysis for microbial marker-gene
      surveys},
    author = {Joseph N. Paulson and Oscar Colin Stine and Hector
      Corrada Bravo and Mihai Pop},
    year = {2013},
    journal = {Nat Meth},
    volume = {advance online publication},
    doi = {10.1038/nmeth.2658},
    url =
      {http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2658.html},
  }

  @Manual{,
    title = {metagenomeSeq: Statistical analysis for sparse
      high-throughput sequncing.},
    author = {Joseph N. Paulson and Nathan D. Olson and Domenick J.
      Braccia and Justin Wagner and Hisham Talukder and Mihai Pop and
      Hector Corrada Bravo},
    year = {2013},
    note = {Bioconductor package},
    url = {http://www.cbcb.umd.edu/software/metagenomeSeq},
  }

  @Article{,
    title = {Longitudinal differential abundance analysis of
      marker-gene surveys using smoothing splines},
    author = {Joseph N. Paulson* and Hisham Talukder* and Hector
      Corrada Bravo},
    year = {2017},
    journal = {biorxiv},
    doi = {10.1101/099457},
    url = {https://www.biorxiv.org/content/10.1101/099457v1},
  }