transomics2cytoscape
This package is for version 3.12 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: 3.12
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).
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 "4.0") 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")| transomics2cytoscape | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, KEGG, Network, Pathways, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | Artistic-2.0 |
| Depends | |
| Imports | RCy3, KEGGREST, dplyr |
| System Requirements | Java 11, Cytoscape 3.8.*, Cy3D >= 1.1.2 |
| URL |
See More
| Suggests | testthat, roxygen2, knitr, BiocStyle, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | transomics2cytoscape_1.0.0.tar.gz |
| Windows Binary | transomics2cytoscape_1.0.0.zip |
| macOS 10.13 (High Sierra) | transomics2cytoscape_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/transomics2cytoscape |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/transomics2cytoscape |
| Bioc Package Browser | https://code.bioconductor.org/browse/transomics2cytoscape/ |
| Package Short Url | https://bioconductor.org/packages/transomics2cytoscape/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |