transomics2cytoscape

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12

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

Bioconductor version: Development (3.24)

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] ORCID: 0000-0001-8501-7319 , Katsuyuki Yugi [aut] ORCID: 0000-0002-2046-4289

Maintainer: Kozo Nishida <kozo.nishida at gmail.com>

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

Kozo Nishida, Katsuyuki Yugi. transomics2cytoscape: A tool set for 3D Trans-Omic network visualization with Cytoscape. doi:10.18129/B9.bioc.transomics2cytoscape, R package version 1.23.0, https://bioconductor.org/packages/transomics2cytoscape.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, KEGG, Network, Pathways, Software
Version	1.23.0
In Bioconductor since	BioC 3.12 (R-4.0) (6 years)
License	Artistic-2.0
Depends
Imports	RCy3, KEGGREST, dplyr, purrr, tibble, pbapply
System Requirements	Cytoscape >= 3.10.0
URL

Suggests	testthat, roxygen2, knitr, BiocStyle, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow 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 (big-sur-x86_64)	transomics2cytoscape_1.23.0.tgz
macOS Binary (sonoma-arm64)	transomics2cytoscape_1.23.0.tgz
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/
Package Downloads Report	Download Stats