DOI: 10.18129/B9.bioc.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>

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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
Suggests RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
URL http://dx.doi.org/10.1038/ncomms3464
Depends On Me Fletcher2013b, RTNduals, RTNsurvival
Imports Me
Suggests Me geneplast
Links To Me
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Source Package RTN_2.24.0.tar.gz
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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/
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