RTN

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see RTN.

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Bioconductor version: 3.13

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 "4.1") 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

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Details

biocViews GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, GraphAndNetwork, Network, NetworkEnrichment, NetworkInference, Software, Transcription

Version 2.16.0

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

URL http://dx.doi.org/10.1038/ncomms3464

Suggests RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown

Linking To

Enhances

Depends On Me Fletcher2013b, RTNduals, RTNsurvival

Imports Me

Suggests Me geneplast

Links To Me

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