To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RTN")
In most cases, you don't need to download the package archive at all.
RTN
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see RTN.
Reconstruction of transcriptional networks and analysis of master regulators
Bioconductor version: 3.3
This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses. Additionally, master regulators can be linked to genetic markers using eQTL/VSE analysis, taking advantage of the haplotype block structure mapped to the human genome in order to explore risk-associated SNPs identified in GWAS studies.
Author: Mauro Castro, Xin Wang, Michael Fletcher, Florian Markowetz and Kerstin Meyer
Maintainer: Mauro Castro <mauro.a.castro at gmail.com>
Citation (from within R,
enter citation("RTN")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RTN")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RTN")
| R Script | Main vignette: reconstruction and analysis of transcriptional networks in R | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, GraphAndNetwork, NetworkAnalysis, NetworkEnrichment, NetworkInference, SNP, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15), methods, igraph |
| Imports | RedeR, minet, snow, limma, data.table, ff, car, IRanges |
| LinkingTo | |
| Suggests | HTSanalyzeR, RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | http://dx.doi.org/10.1038/ncomms3464 |
| Depends On Me | Fletcher2013b |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RTN_1.10.0.tar.gz |
| Windows Binary | RTN_1.10.0.zip |
| Mac OS X 10.9 (Mavericks) | RTN_1.10.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/RTN/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/RTN/ |
| Package Downloads Report | Download Stats |
Documentation »
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