To cite the transomics2cytoscape package in publications use:

  Nishida K, Maruyama J, Kaizu K, Takahashi K and Yugi K.
  Transomics2cytoscape: an automated software for interpretable
  2.5-dimensional visualization of trans-omic networks npj Systems
  Biology and Applications 2024, 10, 16.
  https://doi.org/10.1038/s41540-024-00342-8

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks},
    author = {Kozo Nishida and Junichi Maruyama and Kazunari Kaizu and Koichi Takahashi and Katsuyuki Yugi},
    journal = {npj Systems Biology and Applications},
    year = {2024},
    doi = {10.1038/s41540-024-00342-8},
    url = {https://www.nature.com/articles/s41540-024-00342-8},
    volume = {10},
    pages = {16},
  }