transomics2cytoscape: A tool set for 3D Trans-Omic network visualization with Cytoscape

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).

Package details

AuthorKozo Nishida [aut, cre] (<https://orcid.org/0000-0001-8501-7319>), Katsuyuki Yugi [aut] (<https://orcid.org/0000-0002-2046-4289>)
Bioconductor views DataImport KEGG Network Pathways Software
MaintainerKozo Nishida <kozo.nishida@gmail.com>
LicenseArtistic-2.0
Version1.0.0
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("transomics2cytoscape")

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transomics2cytoscape documentation built on Nov. 8, 2020, 8:14 p.m.