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transomics2cytoscape
This package is for version 3.16 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: 3.16
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年07月02日1) using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4).
Author: Kozo Nishida [aut, cre] , Katsuyuki Yugi [aut]
Maintainer: Kozo Nishida <kozo.nishida at gmail.com>
citation("transomics2cytoscape")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("transomics2cytoscape")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("transomics2cytoscape")
Details
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Follow Installation instructions to use this package in your R session.