Registration and Call for Abstracts Open for Bioc2024

transomics2cytoscape

This is the development version of transomics2cytoscape; for the stable release version, see transomics2cytoscape.

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


Bioconductor version: Development (3.19)

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 (from within R, enter citation("transomics2cytoscape")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews DataImport, KEGG, Network, Pathways, Software
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends
Imports RCy3, KEGGREST, dplyr, purrr, tibble, pbapply
System Requirements Cytoscape >= 3.10.0
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_1.13.0.tar.gz
Windows Binary transomics2cytoscape_1.13.0.zip
macOS Binary (x86_64) transomics2cytoscape_1.13.0.tgz
macOS Binary (arm64)
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