How to cite the Bioconductor package cicero

cicero is a popular Bioconductor package that is available at https://bioconductor.org/packages/cicero. 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 cicero package have suggested.

Example of an in-text citation

Analysis of the data was done using the cicero package (v1.8.1; Pliner et al., 2018).

Reference list entry

Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., Adey, A. C., Steemers, F. J., Shendure, J., & Trapnell, C. (2018). Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data. Molecular Cell, 71(5), 858-871.e8.

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 cicero package v1.8.1 (1).

Reference list entry

1.
Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, et al. Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data. Mol Cell. 2018 Sep;71(5):858-871.e8.

BibTeX

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

BibTeX

@ARTICLE{Pliner2018-gg,
  title     = "Cicero predicts cis-regulatory {DNA} interactions from
               single-cell chromatin accessibility data",
  author    = "Pliner, Hannah A and Packer, Jonathan S and McFaline-Figueroa,
               Jos{\'e} L and Cusanovich, Darren A and Daza, Riza M and
               Aghamirzaie, Delasa and Srivatsan, Sanjay and Qiu, Xiaojie and
               Jackson, Dana and Minkina, Anna and Adey, Andrew C and Steemers,
               Frank J and Shendure, Jay and Trapnell, Cole",
  journal   = "Mol. Cell",
  publisher = "Elsevier BV",
  volume    =  71,
  number    =  5,
  pages     = "858--871.e8",
  month     =  sep,
  year      =  2018,
  url       = "http://dx.doi.org/10.1016/j.molcel.2018.06.044",
  copyright = "http://www.elsevier.com/open-access/userlicense/1.0/",
  language  = "en",
  issn      = "1097-2765, 1097-4164",
  doi       = "10.1016/j.molcel.2018.06.044"
}

RIS

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

RIS

TY  - JOUR
AU  - Pliner, Hannah A
AU  - Packer, Jonathan S
AU  - McFaline-Figueroa, José L
AU  - Cusanovich, Darren A
AU  - Daza, Riza M
AU  - Aghamirzaie, Delasa
AU  - Srivatsan, Sanjay
AU  - Qiu, Xiaojie
AU  - Jackson, Dana
AU  - Minkina, Anna
AU  - Adey, Andrew C
AU  - Steemers, Frank J
AU  - Shendure, Jay
AU  - Trapnell, Cole
TI  - Cicero predicts cis-regulatory DNA interactions from single-cell chromatin
      accessibility data
T2  - Mol. Cell
VL  - 71
IS  - 5
SP  - 858-871.e8
PY  - 2018
DA  - 2018/9
PB  - Elsevier BV
SN  - 1097-2765
DO  - 10.1016/j.molcel.2018.06.044
UR  - http://dx.doi.org/10.1016/j.molcel.2018.06.044
ER  -

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