RCy3
This is the released version of RCy3; for the devel version, see RCy3.
Functions to Access and Control Cytoscape
Bioconductor version: Release (3.23)
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]
, 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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 2.32.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 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, GeneNetworkBuilder, MetaPhOR, MOGAMUN, NCIgraph, regutools, transomics2cytoscape, dendroNetwork, lilikoi, netgsa, ScriptMapR |
| Suggests Me | graphite, rScudo, tidysbml, sharp |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RCy3_2.32.0.tar.gz |
| Windows Binary (x86_64) | RCy3_2.32.0.zip |
| macOS Binary (big-sur-x86_64) | RCy3_2.32.0.tgz |
| macOS Binary (sonoma-arm64) | RCy3_2.32.0.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 |