Registration Open for Bioc2024 July 24-26


RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

RTN: reconstruction of transcriptional regulatory networks and analysis of regulons." HTML R Script
Reference Manual PDF


biocViews GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, GraphAndNetwork, Network, NetworkEnrichment, NetworkInference, Software, Transcription
Version 2.28.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 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
System Requirements
See More
Suggests RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
Linking To
Depends On Me RTNduals, RTNsurvival, Fletcher2013b
Imports Me
Suggests Me geneplast
Links To Me
Build Report Build Report

Package Archives

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

Source Package RTN_2.28.0.tar.gz
Windows Binary
macOS Binary (x86_64) RTN_2.28.0.tgz
macOS Binary (arm64) RTN_2.28.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats