To cite CAGEfightR in publications use:

  Thodberg et al, CAGEfightR: analysis of 5′-end data using
  R/Bioconductor, BMC Bioinformatics, 20, 487. (2019)

A BibTeX entry for LaTeX users is

  @Article{,
    title = {CAGEfightR : analysis of 5 ′ -end data using R / Bioconductor},
    author = {Malte Thodberg and Axel Thieffry and Kristoffer Vitting-Seerup and Robin Andersson and Albin Sandelin},
    year = {2019},
    journal = {BMC Bioinformatics},
    doi = {10.1186/s12859-019-3029-5},
    volume = {20},
    issue = {1},
    pages = {487},
  }