RCy3
Functions to Access and Control Cytoscape
Bioconductor version: Release (3.17)
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.
Author: Alex Pico [aut, cre] 
, Tanja Muetze [aut], Paul Shannon [aut], Ruth Isserlin [ctb], Shraddha Pai [ctb], Julia Gustavsen [ctb], Georgi Kolishovski [ctb], Yihang Xin [ctb]
Maintainer: Alex Pico <alex.pico at gladstone.ucsf.edu>
citation("RCy3")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RCy3")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("RCy3")| 01. Overview of RCy3 ~25 min | HTML | R Script |
| 02. Cytoscape and igraph ~5 min | HTML | R Script |
| 03. Cytoscape and graphNEL ~5 min | HTML | R Script |
| 04. Importing data ~5 min | HTML | R Script |
| 05. Network functions and visualization ~15 min | HTML | R Script |
| 06. Cancer networks and data ~40 min | HTML | R Script |
| 07. Identifier mapping ~20 min | HTML | R Script |
| 08. Upgrading existing scripts ~15 min | HTML | R Script |
| 09. Cytoscape and NDEx ~20 min | HTML | R Script |
| 10. Group nodes ~15 min | HTML | R Script |
| 11. Custom Graphics and Labels ~10 min | HTML | R Script |
| 12. Filtering Networks ~10 min | HTML | R Script |
| 13. Phylogenetic Trees ~3 min | HTML | R Script |
| 14. Jupyter Bridge and RCy3 ~10 min | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization |
| Version | 2.20.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | httr, methods, RJSONIO, XML, utils, BiocGenerics, stats, graph, fs, uuid, uchardet, glue, RCurl, base64url, base64enc, IRkernel, IRdisplay, RColorBrewer, gplots |
| Linking To | |
| Suggests | BiocStyle, knitr, rmarkdown, igraph, grDevices |
| System Requirements | Cytoscape (>= 3.7.1), CyREST (>= 3.8.0) |
| Enhances | |
| URL | https://github.com/cytoscape/RCy3 |
| Bug Reports | https://github.com/cytoscape/RCy3/issues |
See More
| Depends On Me | |
| Imports Me | categoryCompare, CeTF, fedup, MetaPhOR, MOGAMUN, NCIgraph, netZooR, regutools, TimiRGeN, transomics2cytoscape |
| Suggests Me | graphite, netDx, rScudo |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RCy3_2.20.0.tar.gz |
| Windows Binary | RCy3_2.20.0.zip |
| macOS Binary (x86_64) | RCy3_2.20.0.tgz |
| macOS Binary (arm64) | RCy3_2.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RCy3 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RCy3 |
| Bioc Package Browser | https://code.bioconductor.org/browse/RCy3/ |
| Package Short Url | https://bioconductor.org/packages/RCy3/ |
| Package Downloads Report | Download Stats |