transomics2cytoscape

DOI: 10.18129/B9.bioc.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 (3.15)

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 "4.2") and enter:

if (!requireNamespace("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")

 

HTML R Script transomics2cytoscape
PDF   Reference Manual

Details

biocViews DataImport, KEGG, Network, Pathways, Software
Version 1.5.0
In Bioconductor since BioC 3.12 (R-4.0) (1 year)
License Artistic-2.0
Depends
Imports RCy3, KEGGREST, dplyr
LinkingTo
Suggests testthat, roxygen2, knitr, BiocStyle, rmarkdown
SystemRequirements Java 11, Cytoscape 3.8.2, Cy3D >= 1.1.3
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package transomics2cytoscape_1.5.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/transomics2cytoscape
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/transomics2cytoscape
Package Short Url https://bioconductor.org/packages/transomics2cytoscape/
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