transomics2cytoscape

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

Bioconductor version: 3.23 · Package version: 1.22.0

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).

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("transomics2cytoscape")