birte

DOI: 10.18129/B9.bioc.birte    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see birte.

Bayesian Inference of Regulatory Influence on Expression (biRte)

Bioconductor version: 3.8

Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. biRte uses regulatory networks of TFs, miRNAs and possibly other factors, together with mRNA, miRNA and other available expression data to predict the relative influence of a regulator on the expression of its target genes. Inference is done in a Bayesian modeling framework using Markov-Chain-Monte-Carlo. A special feature is the possibility for follow-up network reverse engineering between active regulators.

Author: Holger Froehlich, contributions by Benedikt Zacher

Maintainer: Holger Froehlich <frohlich at bit.uni-bonn.de>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("birte")

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("birte")

 

PDF	R Script	Bayesian Inference of Regulation of Transcriptional Activity
PDF		Reference Manual
Text		README

Details

biocViews	Bayesian, GeneExpression, Microarray, Network, NetworkInference, Regression, Sequencing, Software, Transcription
Version	1.18.0
In Bioconductor since	BioC 3.1 (R-3.2) (4 years)
License	GPL (>= 2)
Depends	R (>= 3.0.0), RcppArmadillo (>= 0.3.6.1), Rcpp
Imports	MASS, limma(>= 3.22.0), glmnet, Biobase, nem, graphics, stats, utils
LinkingTo	RcppArmadillo, Rcpp
Suggests	knitr
SystemRequirements	BLAS, LAPACK
Enhances	Rgraphviz
URL
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Build Report

Package Archives

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

Source Package	birte_1.18.0.tar.gz
Windows Binary	birte_1.18.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	birte_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/birte
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/birte
Package Short Url	http://bioconductor.org/packages/birte/
Package Downloads Report	Download Stats