RCy3
This is thereleased version of RCy3; for the devel version, seeRCy3.
Functions to Access and Control Cytoscape
Bioconductor version: Release (3.22)
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: Jing Chen [cre], Alex Pico [aut]
ORCID: 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]
Maintainer: Jing Chen <jingjingbic at gmail.com>
citation("RCy3")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("RCy3")For older versions of R, please refer to the appropriateBioconductor 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 | 2.30.1 |
| In Bioconductor since | BioC 3.2 (R-3.2) (10 years) |
| License | MIT + fileLICENSE |
| 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,GeneNetworkBuilder,MetaPhOR,MOGAMUN,MSstatsBioNet,NCIgraph,regutools,transomics2cytoscape,dendroNetwork,lilikoi,netgsa,ScriptMapR |
| Suggests Me | graphite,rScudo,tidysbml,sharp |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | RCy3_2.30.1.tar.gz |
| Windows Binary (x86_64) | RCy3_2.30.0.zip (64-bit only) |
| macOS Binary (x86_64) | RCy3_2.30.1.tgz |
| macOS Binary (arm64) | RCy3_2.30.1.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 |
| Old Source Packages for BioC 3.22 | Source Archive |