# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "transomics2cytoscape" in publications use:'
type: software
license: Artistic-2.0
title: 'transomics2cytoscape: A tool set for 3D Trans-Omic network visualization with
  Cytoscape'
version: 1.22.0
doi: 10.1038/s41540-024-00342-8
identifiers:
- type: doi
  value: 10.32614/CRAN.package.transomics2cytoscape
abstract: transomics2cytoscape generates a file for 3D transomics visualization by
  providing input that specifies the IDs of multiple KEGG pathway layers, their corresponding
  Z-axis heights, and an input that represents the edges between the pathway layers.
  The edges are used, for example, to describe the relationships between kinase on
  a pathway and enzyme on another pathway. This package automates creation of a transomics
  network as shown in the figure in Yugi.2014 (https://doi.org/10.1016/j.celrep.2014.07.021)
  using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4).
authors:
- family-names: Nishida
  given-names: Kozo
  email: kozo.nishida@gmail.com
  orcid: https://orcid.org/0000-0001-8501-7319
- family-names: Yugi
  given-names: Katsuyuki
  email: katsuyuki.yugi@riken.jp
  orcid: https://orcid.org/0000-0002-2046-4289
preferred-citation:
  type: article
  title: 'Transomics2cytoscape: an automated software for interpretable 2.5-dimensional
    visualization of trans-omic networks'
  authors:
  - family-names: Nishida
    given-names: Kozo
    email: kozo.nishida@gmail.com
    orcid: https://orcid.org/0000-0001-8501-7319
  - family-names: Maruyama
    given-names: Junichi
  - family-names: Kaizu
    given-names: Kazunari
  - family-names: Takahashi
    given-names: Koichi
  - family-names: Yugi
    given-names: Katsuyuki
    email: katsuyuki.yugi@riken.jp
    orcid: https://orcid.org/0000-0002-2046-4289
  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'
  start: '16'
repository: https://bioc-release.r-universe.dev
commit: 31d9f51ffeee917084250806847c1602ef5ac986
date-released: '2026-04-28'
contact:
- family-names: Nishida
  given-names: Kozo
  email: kozo.nishida@gmail.com
  orcid: https://orcid.org/0000-0001-8501-7319