EmpiricalBrownsMethod
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see EmpiricalBrownsMethod.
Uses Brown's method to combine p-values from dependent tests
Bioconductor version: 3.12
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("EmpiricalBrownsMethod")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Pathways, Software, StatisticalMethod |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.2.0) |
| Imports | |
| System Requirements | |
| URL | https://github.com/IlyaLab/CombiningDependentPvaluesUsingEBM.git |
See More
| Suggests | BiocStyle, testthat, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | poolVIM |
| Imports Me | EBSEA, NADfinder |
| Suggests Me | ActivePathways |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EmpiricalBrownsMethod_1.18.0.tar.gz |
| Windows Binary | EmpiricalBrownsMethod_1.18.0.zip |
| macOS 10.13 (High Sierra) | EmpiricalBrownsMethod_1.18.0.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 |
| Old Source Packages for BioC 3.12 | Source Archive |