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 (from within R, enter 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 PDF R Script
Reference Manual PDF

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