How to cite the R package sequenza

sequenza is a popular R package that is available at https://cran.r-project.org/web/packages/sequenza/index.html. 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 sequenza package have suggested.

Example of an in-text citation

Analysis of the data was done using the sequenza package (v3.0.0; Favero et al., 2015).

Reference list entry

Favero, F., Joshi, T., Marquard, A. M., Birkbak, N. J., Krzystanek, M., Li, Q., Szallasi, Z., & Eklund, A. C. (2015). Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Annals of Oncology, 26(1), 64–70.

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 sequenza package v3.0.0 (1).

Reference list entry

1.
Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, et al. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol. 2015 Jan;26(1):64–70.

BibTeX

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

BibTeX

@ARTICLE{Favero2015-uf,
  title     = "Sequenza: allele-specific copy number and mutation profiles from
               tumor sequencing data",
  author    = "Favero, F and Joshi, T and Marquard, A M and Birkbak, N J and
               Krzystanek, M and Li, Q and Szallasi, Z and Eklund, A C",
  journal   = "Ann. Oncol.",
  publisher = "Elsevier BV",
  volume    =  26,
  number    =  1,
  pages     = "64--70",
  month     =  jan,
  year      =  2015,
  url       = "http://dx.doi.org/10.1093/annonc/mdu479",
  copyright = "http://creativecommons.org/licenses/by-nc/4.0/",
  language  = "en",
  issn      = "0923-7534, 1569-8041",
  doi       = "10.1093/annonc/mdu479"
}

RIS

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

RIS

TY  - JOUR
AU  - Favero, F
AU  - Joshi, T
AU  - Marquard, A M
AU  - Birkbak, N J
AU  - Krzystanek, M
AU  - Li, Q
AU  - Szallasi, Z
AU  - Eklund, A C
TI  - Sequenza: allele-specific copy number and mutation profiles from tumor
      sequencing data
T2  - Ann. Oncol.
VL  - 26
IS  - 1
SP  - 64-70
PY  - 2015
DA  - 2015/1
PB  - Elsevier BV
SN  - 0923-7534
DO  - 10.1093/annonc/mdu479
UR  - http://dx.doi.org/10.1093/annonc/mdu479
ER  -

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sequenza R package release history

Version	Release date
2.1.2	2015-10-10
2.1.1	2015-01-27
2.1.0	2014-10-08
2.0.0	2014-04-08
1.0.5	2014-02-11
1.0.4	2014-01-20
1.0.3	2013-12-12
1.0.2	2013-12-05
1.0.1	2013-12-02