RCy3
Functions to Access and Control Cytoscape
Bioconductor version: Release (3.19)
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 "4.4") 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 | 2.24.0 |
In Bioconductor since | BioC 3.2 (R-3.2) (9 years) |
License | MIT + file LICENSE |
Depends | |
Imports | httr, methods, RJSONIO, XML, utils, BiocGenerics, stats, graph, fs, uuid, stringi, glue, RCurl, base64url, base64enc, IRkernel, IRdisplay, RColorBrewer, gplots |
System Requirements | Cytoscape (>= 3.7.1), CyREST (>= 3.8.0) |
URL | https://github.com/cytoscape/RCy3 |
Bug Reports | https://github.com/cytoscape/RCy3/issues |
See More
Suggests | BiocStyle, knitr, rmarkdown, igraph, grDevices |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | categoryCompare, CeTF, enrichViewNet, fedup, MetaPhOR, MOGAMUN, NCIgraph, netZooR, regutools, transomics2cytoscape, dendroNetwork, lilikoi, mappeR, netgsa, ScriptMapR |
Suggests Me | graphite, netDx, rScudo, sharp |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | RCy3_2.24.0.tar.gz |
Windows Binary | RCy3_2.24.0.zip |
macOS Binary (x86_64) | RCy3_2.24.0.tgz |
macOS Binary (arm64) | RCy3_2.24.0.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 |