RTN
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see RTN.
Reconstruction of transcriptional networks and analysis of master regulators
Bioconductor version: 3.8
This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses. Additionally, master regulators can be linked to genetic markers using eQTL/VSE analysis, taking advantage of the haplotype block structure mapped to the human genome in order to explore risk-associated SNPs identified in GWAS studies.
Author: Mauro Castro, Xin Wang, Michael Fletcher, Florian Markowetz and Kerstin Meyer
Maintainer: Mauro Castro <mauro.a.castro at gmail.com>
citation("RTN")):
Installation
To install this package, start R (version "3.5") 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 networks and analysis of master regulators." | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, GraphAndNetwork, NetworkEnrichment, NetworkInference, SNP, Software |
| Version | 2.6.3 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3.3), methods |
| Imports | RedeR, minet, viper, mixtools, snow, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment |
| System Requirements | |
| URL | http://dx.doi.org/10.1038/ncomms3464 |
See More
| Suggests | RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | Fletcher2013b, RTNduals, RTNsurvival |
| 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_2.6.3.tar.gz |
| Windows Binary | RTN_2.6.3.zip |
| Mac OS X 10.11 (El Capitan) | RTN_2.6.3.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 |
| Old Source Packages for BioC 3.8 | Source Archive |