transomics2cytoscape
A tool set for 3D Trans-Omic network visualization with Cytoscape
Bioconductor version: 3.24 · Package version: 1.23.0
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).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("transomics2cytoscape")Details
| Maintainer | Kozo Nishida <kozo.nishida@gmail.com> |
| Author | Kozo Nishida [aut, cre] (ORCID: <https://orcid.org/0000-0001-8501-7319>), Katsuyuki Yugi [aut] (ORCID: <https://orcid.org/0000-0002-2046-4289>) |
| License | Artistic-2.0 |
| System Requirements | Cytoscape >= 3.10.0 |
| Downloads rank | 336 |
| Source branch | devel |
| biocViews | DataImport, KEGG, Network, Pathways, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | transomics2cytoscape_1.23.0.tar.gz |
| Windows binary (x86_64) | transomics2cytoscape_1.23.0.zip |
| macOS binary (arm64) | transomics2cytoscape_1.23.0.tgz |
| macOS binary (x86_64) | transomics2cytoscape_1.23.0.tgz |