transomics2cytoscape
This is the released version of transomics2cytoscape; for the devel version, see transomics2cytoscape.
A tool set for 3D Trans-Omic network visualization with Cytoscape
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.22.0 |
| 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 |
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_1.22.0.tar.gz |
| Windows Binary (x86_64) | transomics2cytoscape_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | transomics2cytoscape_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | transomics2cytoscape_1.22.0.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 |