To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RTN")
In most cases, you don't need to download the package archive at all.
RTN
Reconstruction of transcriptional networks and analysis of master regulators
Bioconductor version: 3.0
This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses. Additionally, master regulators can be linked to genetic markers using eQTL/VSE analysis, taking advantage of the haplotype block structure mapped to the human genome in order to explore risk-associated SNPs identified in GWAS studies.
Author: Mauro Castro, Xin Wang, Michael Fletcher, Florian Markowetz and Kerstin Meyer
Maintainer: Mauro Castro <mauro.a.castro at gmail.com>
Citation (from within R,
enter citation("RTN")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RTN")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RTN")
| R Script | Main vignette: reconstruction and analysis of transcriptional networks in R | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, GraphAndNetwork, NetworkAnalysis, NetworkEnrichment, NetworkInference, SNP, Software |
| Version | 1.4.1 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15), methods, igraph |
| Imports | RedeR, minet, snow, limma, data.table, ff, car, IRanges |
| LinkingTo | |
| Suggests | HTSanalyzeR, RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | http://dx.doi.org/10.1038/ncomms3464 |
| Depends On Me | Fletcher2013b |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RTN_1.4.1.tar.gz |
| Windows Binary | RTN_1.4.1.zip |
| Mac OS X 10.6 (Snow Leopard) | RTN_1.4.1.tgz |
| Mac OS X 10.9 (Mavericks) | RTN_1.4.1.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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