To cite the R package 'Chicago' in publications use:

  Cairns J*, Freire-Pritchett P*, Wingett SW, Dimond A, Plagnol V,
  Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov
  M CHiCAGO: Robust Detection of DNA Looping Interactions in Capture
  Hi-C data, Genome Biology (2016) 17:127, doi:
  https://doi.org/10.1186/s13059-016-0992-2

A BibTeX entry for LaTeX users is

  @Article{,
    title = {CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data},
    author = {Jonathan Cairns and Paula Freire-Pritchett and Steven W Wingett and Andrew Dimond and Vincent Plagnol and Daniel Zerbino and Stefan Schoenfelder and Biola-Maria Javierre and Cameron Osborne and Peter Fraser and Mikhail Spivakov},
    journal = {Genome Biology},
    year = {2016},
    volume = {17},
    pages = {127},
    note = {R package version 4.4.1},
  }