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This is the development version of transomics2cytoscape; for the stable release version, see transomics2cytoscape.

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

Bioconductor version: Development (3.20)

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>

Citation (from within R, enter citation("transomics2cytoscape")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

transomics2cytoscape HTML R Script
Reference Manual PDF


biocViews DataImport, KEGG, Network, Pathways, Software
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Imports RCy3, KEGGREST, dplyr, purrr, tibble, pbapply
System Requirements Cytoscape >= 3.10.0
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Suggests testthat, roxygen2, knitr, BiocStyle, rmarkdown
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Follow Installation instructions to use this package in your R session.

Source Package transomics2cytoscape_1.15.0.tar.gz
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macOS Binary (x86_64) transomics2cytoscape_1.15.0.tgz
macOS Binary (arm64) transomics2cytoscape_1.15.0.tgz
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