birte

DOI: 10.18129/B9.bioc.birte    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of birte; to use it, please install the devel version of Bioconductor.

Bayesian Inference of Regulatory Influence on Expression (biRte)

Bioconductor version: Development (3.10)

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>

Citation (from within R, enter citation("birte")):

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("birte")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews Bayesian, GeneExpression, Microarray, Network, NetworkInference, Regression, Sequencing, Software, Transcription
Version 1.21.1
In Bioconductor since BioC 3.1 (R-3.2) (4.5 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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary birte_1.21.1.zip
Mac OS X 10.11 (El Capitan)
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 https://bioconductor.org/packages/birte/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: