To cite MPRAnalyze in publications use:

  Ashuach, T., Fischer, D. S., Kreimer, A., Ahituv, N., Theis, F. J., &
  Yosef, N. (2019).  MPRAnalyze: statistical framework for massively
  parallel reporter assays. Genome biology, 20(1), 1-17.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {MPRAnalyze: statistical framework for massively parallel reporter assays},
    author = {Tal Ashuach and David S. Fischer and Anat Kreimer and Nadav Ahituv and Nir Yosef},
    journal = {Genome Biology},
    year = {2019},
    volume = {20},
    number = {1},
    pages = {1--17},
    url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1787-z},
  }