RCy3
Functions to Access and Control Cytoscape
Bioconductor version: 3.23 · Package version: 2.32.0
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) |
| Downloads rank | 1217 |
| Source branch | RELEASE_3_23 |
| biocViews | GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization |
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
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