DOI: 10.18129/B9.bioc.transomics2cytoscape    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see transomics2cytoscape.

A tool set for 3D Trans-Omic network visualization with Cytoscape

Bioconductor version: 3.12

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 ( using Cytoscape automation (

Author: Kozo Nishida [aut, cre] , Katsuyuki Yugi [aut]

Maintainer: Kozo Nishida <kozo.nishida at>

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biocViews DataImport, KEGG, Network, Pathways, Software
Version 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (0.5 years)
License Artistic-2.0
Imports RCy3, KEGGREST, dplyr
Suggests testthat, roxygen2, knitr, BiocStyle, rmarkdown
SystemRequirements Java 11, Cytoscape 3.8.*, Cy3D >= 1.1.2
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