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Protocols

bridge specifications

Information


Unique identifier OMICS_01996
Name bridge
Alternative name Bayesian Robust Inference for Differential Gene Expression
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.44.0
Stability Stable
Requirements
R(>=1.9.0), rama
Maintained Yes

Versioning


No version available

Documentation


bridge citations

 (4)
library_books

Robust volcano plot: identification of differential metabolites in the presence of outliers

2018
BMC Bioinformatics
PMCID: 5896081
PMID: 29642836
DOI: 10.1186/s12859-018-2117-2

[…] , (ii) classical non-parametric approaches, such as significance analysis of microarrays (SAM) [], and the Wilcoxon [] and Kruskal-Wallis (K-W) [] tests, (iii) Bayesian parametric approaches, such as Bayesian robust inference for differential gene expression (BRIDGE) [], empirical Bayes methods for microarrays (EBarrays) [], and linear models for microarrays (Limma) [], and (iv) Bayesian non-param […]

library_books

Robust Modeling of Differential Gene Expression Data Using Normal/Independent Distributions: A Bayesian Approach

2015
PLoS One
PMCID: 4409222
PMID: 25910040
DOI: 10.1371/journal.pone.0123791

[…] ng Markov Chain Monte Carlo (MCMC), were applied by [, ]. [, ] introduced a hierarchical t distribution formulation which is more robust to outliers than the normal model. [] call their model BRIDGE (Bayesian Robust Inference for Differential Gene Expression). BRIDGE (2013, http://www.rglab.org) has been recently constructed as a package consisting of several functions in R software for testing di […]

library_books

Non Parametric Change Point Method for Differential Gene Expression Detection

2011
PLoS One
PMCID: 3104986
PMID: 21655325
DOI: 10.1371/journal.pone.0020060

[…] , a Bayesian model for DGE patterns of the DosR regulon of Mycobacterium tuberculosis in the timing of gene induction . With respect to DGE analysis, there are BRIDGE (Bayesian robust inference for differential gene expression) for DGE detection in microarrays with small sample sizes , and DGE detecting method LRS (likelihood ratio te […]

call_split

MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis

2008
Genome Biol
PMCID: 2530872
PMID: 18652698
DOI: 10.1186/gb-2008-9-7-r118
call_split See protocol

[…] estimates of expression intensities from two-color microarray data, which typically consist of a few replicates and potential outliers []. RAMA also takes advantage of dye swap experimental designs. Bayesian Robust Inference for Differential Gene Expression (BRIDGE) is a robust algorithm that selects differentially expressed genes under different experimental conditions on both one- and two-color […]


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