bridge

DOI: 10.18129/B9.bioc.bridge  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.16 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: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	bridge Tutorial
PDF		Reference Manual

Details

biocViews	DifferentialExpression, Microarray, OneChannel, Software, TwoChannel
Version	1.62.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18 years)
License	GPL (>= 2)
Depends	R (>= 1.9.0), rama
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	bridge_1.62.0.tar.gz
Windows Binary	bridge_1.62.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/bridge
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bridge
Package Short Url	https://bioconductor.org/packages/bridge/
Package Downloads Report	Download Stats