RCy3
Functions to Access and Control Cytoscape
Bioconductor version: 3.23 · Package version: 2.32.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RCy3")Details
| Maintainer | Jing Chen <jingjingbic@gmail.com> |
| Author | Jing Chen [cre], Alex Pico [aut] (ORCID: <https://orcid.org/0000-0001-5706-2163>), Tanja Muetze [aut], Paul Shannon [aut], Ruth Isserlin [ctb], Shraddha Pai [ctb], Julia Gustavsen [ctb], Georgi Kolishovski [ctb], Yihang Xin [ctb] |
| License | MIT + file LICENSE |
| URL | https://github.com/cytoscape/RCy3 |
| Bug Reports | https://github.com/cytoscape/RCy3/issues |
| System Requirements | Cytoscape (>= 3.7.1), CyREST (>= 3.8.0) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization |
| Package Short Url | https://bioconductor.org/packages/RCy3/ |
Citation
From within R, enter citation("RCy3"):
Alex Pico, Tanja Muetze, Paul Shannon. RCy3: Functions to Access and Control Cytoscape. doi:10.18129/B9.bioc.RCy3, R package version 2.32.0, https://bioconductor.org/packages/RCy3.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Overview of RCy3
- Cytoscape and igraph
- Cytoscape and graphNEL
- Importing data
- Network functions and visualization
- Cancer networks and data
- Identifier mapping
- Upgrading existing scripts
- Cytoscape and NDEx
- Group nodes
- Custom Graphics and Labels
- Filtering Networks
- Phylogenetic-trees
- Jupyter Bridge and RCy3
Download
Follow the installation instructions to use this package in your R session.
| Source package | RCy3_2.32.0.tar.gz |
| Windows binary (x86_64) | RCy3_2.32.0.zip |
| macOS binary (arm64) | RCy3_2.32.0.tgz |
| macOS binary (x86_64) | RCy3_2.32.0.tgz |
Dependencies
Imports: httr, methods, RJSONIO, XML, utils, BiocGenerics, stats, graph, fs, uuid, stringi, glue, RCurl, base64url, base64enc, IRkernel, IRdisplay, RColorBrewer, gplots
Reverse dependencies
Imports Me (15): categoryCompare, CeTF, dendroNetwork, enrichViewNet, fedup, GeneNetworkBuilder, lilikoi, MetaPhOR, MOGAMUN, NCIgraph, netgsa, netZooR, regutools, ScriptMapR, transomics2cytoscape