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source("http://bioconductor.org/biocLite.R")
biocLite("GRENITS")
In most cases, you don't need to download the package archive at all.
GRENITS
Gene Regulatory Network Inference Using Time Series
Bioconductor version: 3.0
The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model.
Author: Edward Morrissey
Maintainer: Edward Morrissey <edward.morrissey at gmail.com>
Citation (from within R,
enter citation("GRENITS")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GRENITS")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GRENITS")
| R Script | GRENITS | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bayesian, GeneExpression, GeneRegulation, GraphAndNetwork, Network, NetworkInference, Software, TimeCourse |
| Version | 1.18.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL (>= 2) |
| Depends | R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) |
| Imports | graphics, grDevices, reshape2, stats, utils |
| LinkingTo | Rcpp, RcppArmadillo |
| Suggests | network |
| 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 | GRENITS_1.18.0.tar.gz |
| Windows Binary | GRENITS_1.18.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | GRENITS_1.18.0.tgz |
| Mac OS X 10.9 (Mavericks) | GRENITS_1.18.0.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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