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RTN

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Bioconductor version: Release (3.17)

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>

Citation (from within R, enter citation("RTN")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("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")
RTN: reconstruction of transcriptional regulatory networks and analysis of regulons." HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, GraphAndNetwork, Network, NetworkEnrichment, NetworkInference, Software, Transcription
Version 2.24.0
In Bioconductor since BioC 2.13 (R-3.0) (10 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
Linking To
Suggests RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
System Requirements
Enhances
URL http://dx.doi.org/10.1038/ncomms3464
See More
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_2.24.0.tar.gz
Windows Binary RTN_2.24.0.zip
macOS Binary (x86_64) RTN_2.24.0.tgz
macOS Binary (arm64) RTN_2.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RTN
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RTN
Bioc Package Browser https://code.bioconductor.org/browse/RTN/
Package Short Url https://bioconductor.org/packages/RTN/
Package Downloads Report Download Stats