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EmpiricalBrownsMethod

This is the development version of EmpiricalBrownsMethod; for the stable release version, see EmpiricalBrownsMethod.

Uses Brown's method to combine p-values from dependent tests

Bioconductor version: Development (3.18)

Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.

Author: William Poole

Maintainer: David Gibbs <dgibbs at systemsbiology.org>

Citation (from within R, enter citation("EmpiricalBrownsMethod")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("EmpiricalBrownsMethod")

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("EmpiricalBrownsMethod")
Empirical Browns Method HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, Pathways, Software, StatisticalMethod
Version 1.29.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 years)
License MIT + file LICENSE
Depends R (>= 3.2.0)
Imports
Linking To
Suggests BiocStyle, testthat, knitr, rmarkdown
System Requirements
Enhances
URL https://github.com/IlyaLab/CombiningDependentPvaluesUsingEBM.git
See More
Depends On Me poolVIM
Imports Me EBSEA, NADfinder
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package EmpiricalBrownsMethod_1.29.0.tar.gz
Windows Binary EmpiricalBrownsMethod_1.29.0.zip (64-bit only)
macOS Binary (x86_64) EmpiricalBrownsMethod_1.29.0.tgz
macOS Binary (arm64) EmpiricalBrownsMethod_1.29.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/EmpiricalBrownsMethod
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EmpiricalBrownsMethod
Bioc Package Browser https://code.bioconductor.org/browse/EmpiricalBrownsMethod/
Package Short Url https://bioconductor.org/packages/EmpiricalBrownsMethod/
Package Downloads Report Download Stats