bridge
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see bridge.
Bayesian Robust Inference for Differential Gene Expression
Bioconductor version: 3.9
Test for differentially expressed genes with microarray data. This package can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space.
Author: Raphael Gottardo
Maintainer: Raphael Gottardo <raph at stat.ubc.ca>
citation("bridge")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("bridge")
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("bridge")| bridge Tutorial | R Script | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, Microarray, OneChannel, Software, TwoChannel |
| Version | 1.48.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19 years) |
| License | GPL (>= 2) |
| Depends | R (>= 1.9.0), rama |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| 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 | bridge_1.48.0.tar.gz |
| Windows Binary | bridge_1.48.0.zip |
| Mac OS X 10.11 (El Capitan) | bridge_1.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/bridge |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/bridge |
| Bioc Package Browser | https://code.bioconductor.org/browse/bridge/ |
| Package Short Url | https://bioconductor.org/packages/bridge/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |