To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("birte")
In most cases, you don't need to download the package archive at all.
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Bioconductor version: Release (3.4)
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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("birte")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("birte")
R Script | Bayesian Inference of Regulation of Transcriptional Activity | |
Reference Manual | ||
Text | README |
biocViews | Bayesian, GeneExpression, Microarray, Network, NetworkInference, Regression, Sequencing, Software, Transcription |
Version | 1.10.0 |
In Bioconductor since | BioC 3.1 (R-3.2) (2 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 | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | birte_1.10.0.tar.gz |
Windows Binary | birte_1.10.0.zip (32- & 64-bit) |
Mac OS X 10.9 (Mavericks) | birte_1.10.0.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/birte/tree/release-3.4 |
Package Short Url | http://bioconductor.org/packages/birte/ |
Package Downloads Report | Download Stats |
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