To cite 'cliqueMS' package in publications use:

  O. Senan, A. Aguilar-Mogas, M. Navarro, O. Yanes, R. Guimerà M.
  Sales-Pardo et al. CliqueMS: a computational tool for annotating
  in-source metabolite ions from LC-MS untargeted metabolomics data
  based on a coelution similarity network Bioinformatics, (2019),

A BibTeX entry for LaTeX users is

  @Article{,
    author = {O. Senan and A. Aguilar-Mogas and M. Navarro and J. Capellades and L Noon and D Burks and O. Yanes and R. Guimerà and M. Sales-Pardo},
    title = {CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network},
    journal = {Bioinformatics},
    year = {2019},
    month = {March},
    volume = {35},
    issue = {20},
    url = {https://doi.org/10.1093/bioinformatics/btz207},
  }