RCy3
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see RCy3.
Functions to Access and Control Cytoscape
Bioconductor version: 3.8
Vizualize, analyze and explore networks using Cytoscape via R.
Author: Alexander Pico, Tanja Muetze, Ruth Isserlin, Shraddha Pai, Julia Gustavsen, Georgi Kolishovski, Paul Shannon
Maintainer: Alexander Pico <alex.pico at gladstone.ucsf.edu>, Tanja Muetze <tanja.muetze14 at alumni.imperial.ac.uk>, Paul Shannon <pshannon at systemsbiology.org>
citation("RCy3")):
Installation
To install this package, start R (version "3.5") 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 |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization |
| Version | 2.2.9 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5) |
| Imports | httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph, stats, graph, R.utils |
| System Requirements | Cytoscape (>= 3.7.0), CyREST (>= 3.8.0) |
| URL | https://github.com/cytoscape/RCy3 |
| Bug Reports | https://github.com/cytoscape/RCy3/issues |
See More
| Suggests | RUnit, RColorBrewer, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | categoryCompare, NCIgraph |
| Suggests Me | graphite |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RCy3_2.2.9.tar.gz |
| Windows Binary | RCy3_2.2.9.zip |
| Mac OS X 10.11 (El Capitan) | RCy3_2.2.9.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 3.8 | Source Archive |