RTN

DOI: 10.18129/B9.bioc.RTN    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see RTN.

Reconstruction of transcriptional networks and analysis of master regulators

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("RTN")

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("RTN")

 

HTML	R Script	RTN: reconstruction of transcriptional networks and analysis of master regulators."
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, GraphAndNetwork, NetworkEnrichment, NetworkInference, SNP, Software
Version	2.6.3
In Bioconductor since	BioC 2.13 (R-3.0) (5.5 years)
License	Artistic-2.0
Depends	R (>= 3.3.3), methods
Imports	RedeR, minet, viper, mixtools, snow, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment
LinkingTo
Suggests	RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	http://dx.doi.org/10.1038/ncomms3464
Depends On Me	Fletcher2013b, RTNduals, RTNsurvival
Imports Me
Suggests Me	geneplast
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RTN_2.6.3.tar.gz
Windows Binary	RTN_2.6.3.zip
Mac OS X 10.11 (El Capitan)	RTN_2.6.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RTN
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RTN
Package Short Url	http://bioconductor.org/packages/RTN/
Package Downloads Report	Download Stats