RTN

DOI: 10.18129/B9.bioc.RTN    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RTN.

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Bioconductor version: 3.12

A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.

Author: Clarice Groeneveld [ctb], Gordon Robertson [ctb], Xin Wang [aut], Michael Fletcher [aut], Florian Markowetz [aut], Kerstin Meyer [aut], and Mauro Castro [aut]

Maintainer: Mauro Castro <mauro.a.castro at gmail.com>

Installation

To install this package, start R (version "4.0") 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 regulatory networks and analysis of regulons."
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, GraphAndNetwork, Network, NetworkEnrichment, NetworkInference, Software, Transcription
Version	2.14.1
In Bioconductor since	BioC 2.13 (R-3.0) (7.5 years)
License	Artistic-2.0
Depends	R (>= 3.6.3), methods
Imports	RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils
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_2.14.1.tar.gz
Windows Binary	RTN_2.14.1.zip
macOS 10.13 (High Sierra)	RTN_2.14.1.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	https://bioconductor.org/packages/RTN/
Package Downloads Report	Download Stats