How to cite the Bioconductor package phyloseq

phyloseq is a popular Bioconductor package that is available at https://bioconductor.org/packages/phyloseq. By citing R packages in your paper you lay the grounds for others to be able to reproduce your analysis and secondly you are acknowledging the time and work people have spent creating the package.

APA citation

Formatted according to the APA Publication Manual 7^th edition. Simply copy it to the References page as is.

APA

The minimal requirement is to cite the R package in text along with the version number. Additionally, you can include the reference list entry the authors of the phyloseq package have suggested.

Example of an in-text citation

Analysis of the data was done using the phyloseq package (v1.34.0; McMurdie & Holmes, 2013).

Reference list entry

McMurdie, P. J., & Holmes, S. (2013). Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PloS One, 8(4), e61217.

Vancouver citation

Formatted according to Vancouver style. Simply copy it to the references section as is.

Vancouver

Example of an in-text citation

Analysis of the data was done using the phyloseq package v1.34.0 (1).

Reference list entry

1.
McMurdie PJ, Holmes S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013 Apr 22;8(4):e61217.

BibTeX

Reference entry in BibTeX format. Simply copy it to your favorite citation manager.

BibTeX

@ARTICLE{McMurdie2013-bv,
  title     = "Phyloseq: An {R} package for reproducible interactive analysis
               and graphics of microbiome census data",
  author    = "McMurdie, Paul J and Holmes, Susan",
  journal   = "PLoS One",
  publisher = "Public Library of Science (PLoS)",
  volume    =  8,
  number    =  4,
  pages     = "e61217",
  month     =  apr,
  year      =  2013,
  url       = "http://dx.doi.org/10.1371/journal.pone.0061217",
  language  = "en",
  issn      = "1932-6203",
  doi       = "10.1371/journal.pone.0061217"
}

RIS

Reference entry in RIS format. Simply copy it to your favorite citation manager.

RIS

TY  - JOUR
AU  - McMurdie, Paul J
AU  - Holmes, Susan
TI  - Phyloseq: An R package for reproducible interactive analysis and graphics
      of microbiome census data
T2  - PLoS One
VL  - 8
IS  - 4
SP  - e61217
PY  - 2013
DA  - 2013/4/22
PB  - Public Library of Science (PLoS)
SN  - 1932-6203
DO  - 10.1371/journal.pone.0061217
UR  - http://dx.doi.org/10.1371/journal.pone.0061217
ER  -

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