birte
This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see birte.
Bayesian Inference of Regulatory Influence on Expression (biRte)
Bioconductor version: 3.7
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("birte")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("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")| Bayesian Inference of Regulation of Transcriptional Activity | R Script | |
| Reference Manual | ||
| README | Text |
Details
| biocViews | Bayesian, GeneExpression, Microarray, Network, NetworkInference, Regression, Sequencing, Software, Transcription |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 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 |
| System Requirements | BLAS, LAPACK |
| URL |
See More
| Suggests | knitr |
| Linking To | RcppArmadillo, Rcpp |
| Enhances | Rgraphviz |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | birte_1.16.0.tar.gz |
| Windows Binary | birte_1.16.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | birte_1.16.0.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 | https://bioconductor.org/packages/birte/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |