RTN
This is the development version of RTN; for the stable release version, see RTN.
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
DOI: 10.18129/B9.bioc.RTN
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("RTN")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text |
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 |
See More
| Suggests | RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| 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_2.37.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/RTN/ |
| Package Short Url | https://bioconductor.org/packages/RTN/ |
| Package Downloads Report | Download Stats |