To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("birta")
In most cases, you don't need to download the package archive at all.
birta
Bayesian Inference of Regulation of Transcriptional Activity
Bioconductor version: 3.0
Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. birta (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of TFs and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.
Author: Benedikt Zacher, Khalid Abnaof, Stephan Gade, Erfan Younesi, Achim Tresch, Holger Froehlich
Maintainer: Benedikt Zacher <zacher at lmb.uni-muenchen.de>, Holger Froehlich <frohlich at bit.uni-bonn.de>
Citation (from within R,
enter citation("birta")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("birta")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("birta")
| R Script | Bayesian Inference of Regulation of Transcriptional Activity | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, GraphAndNetwork, Microarray, Sequencing, Software, Transcription |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | GPL (>= 2) |
| Depends | limma, MASS, R (>= 2.10), Biobase, methods |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | birta_1.10.0.tar.gz |
| Windows Binary | birta_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | birta_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | birta_1.10.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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