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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RCytoscape")
In most cases, you don't need to download the package archive at all.
RCytoscape
Display and manipulate graphs in Cytoscape
Bioconductor version: 3.0
Interactvive viewing and exploration of graphs, connecting R to Cytoscape.
Author: Paul Shannon
Maintainer: Paul Shannon <pshannon at fhcrc.org>
Citation (from within R,
enter citation("RCytoscape")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RCytoscape")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RCytoscape")
| R Script | RCytoscape Overview | |
| Reference Manual | ||
| Text | README | |
| Text | NEWS |
Details
| biocViews | GraphAndNetwork, Software, ThirdPartyClient, Visualization |
| Version | 1.16.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) |
| License | GPL-2 |
| Depends | R (>= 2.14.0), graph(>= 1.31.0), XMLRPC (>= 0.2.4) |
| Imports | methods, XMLRPC, BiocGenerics |
| LinkingTo | |
| Suggests | RUnit |
| SystemRequirements | |
| Enhances | |
| URL | http://rcytoscape.systemsbiology.net |
| Depends On Me | |
| Imports Me | categoryCompare, NCIgraph, RamiGO |
| Suggests Me | clipper, GeneNetworkBuilder, graphite, mmnet, NetPathMiner |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RCytoscape_1.16.0.tar.gz |
| Windows Binary | RCytoscape_1.16.0.zip |
| Mac OS X 10.6 (Snow Leopard) | RCytoscape_1.16.0.tgz |
| Mac OS X 10.9 (Mavericks) | RCytoscape_1.16.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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