RTN

This is the development version of RTN; for the stable release version, see RTN.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Bioconductor version: Development (3.24)

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")):

Xin Wang, Michael Fletcher, Florian Markowetz, Kerstin Meyer, and Mauro Castro. RTN: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons. doi:10.18129/B9.bioc.RTN, R package version 2.37.0, https://bioconductor.org/packages/RTN.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, GraphAndNetwork, Network, NetworkEnrichment, NetworkInference, Software, Transcription
Version	2.37.0
In Bioconductor since	BioC 2.13 (R-3.0) (13 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
System Requirements
URL	http://dx.doi.org/10.1038/ncomms3464

Suggests	RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me	RTNduals, RTNsurvival
Imports Me
Suggests Me	geneplast
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	RTN_2.37.0.tar.gz
Windows Binary (x86_64)	RTN_2.37.0.zip
macOS Binary (big-sur-x86_64)	RTN_2.37.0.tgz
macOS Binary (sonoma-arm64)	RTN_2.37.0.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