To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RedeR")
In most cases, you don't need to download the package archive at all.
RedeR
Interactive visualization and manipulation of nested networks
Bioconductor version: 3.0
RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of modular structures, nested networks and multiple levels of hierarchical associations.
Author: Mauro Castro, Xin Wang, Florian Markowetz
Maintainer: Mauro Castro <mauro.a.castro at gmail.com>
Citation (from within R,
enter citation("RedeR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RedeR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RedeR")
| R Script | Main vignette: interactive visualization and manipulation of nested networks | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataRepresentation, GraphAndNetwork, Infrastructure, Network, Software, Visualization |
| Version | 1.14.10 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL (>= 2) |
| Depends | R (>= 2.15), methods, igraph |
| Imports | RCurl, XML |
| LinkingTo | |
| Suggests | PANR, pvclust |
| SystemRequirements | Java Runtime Environment (>= 6) |
| Enhances | |
| URL | http://genomebiology.com/2012/13/4/R29 |
| Depends On Me | Fletcher2013b |
| Imports Me | Mulder2012, RTN |
| Suggests Me | PANR |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RedeR_1.14.10.tar.gz |
| Windows Binary | RedeR_1.14.10.zip |
| Mac OS X 10.6 (Snow Leopard) | RedeR_1.14.10.tgz |
| Mac OS X 10.9 (Mavericks) | RedeR_1.14.10.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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