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 (3.20)
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 "4.4") 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 | ||
NEWS | Text |
Details
biocViews | DataImport, KEGG, Network, Pathways, Software |
Version | 1.15.0 |
In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.15.0.tar.gz |
Windows Binary | transomics2cytoscape_1.15.0.zip |
macOS Binary (x86_64) | transomics2cytoscape_1.15.0.tgz |
macOS Binary (arm64) | transomics2cytoscape_1.15.0.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 |