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bacon

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

Controlling bias and inflation in association studies using the empirical null distribution

Bioconductor version: Development (3.18)

Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.

Author: Maarten van Iterson [aut, cre], Erik van Zwet [ctb]

Maintainer: Maarten van Iterson <mviterson at gmail.com>

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

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("bacon")

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("bacon")
Controlling bias and inflation in association studies using the empirical null distribution HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Bayesian, GenomeWideAssociation, ImmunoOncology, MethylationArray, MultipleComparison, RNASeq, Regression, Software, StatisticalMethod, Transcriptomics
Version 1.29.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 years)
License GPL (>= 2)
Depends R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse
Imports
Linking To
Suggests BiocStyle, knitr, rmarkdown, testthat, roxygen2
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package bacon_1.29.0.tar.gz
Windows Binary bacon_1.29.0.zip
macOS Binary (x86_64) bacon_1.29.0.tgz
macOS Binary (arm64) bacon_1.29.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/bacon
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bacon
Bioc Package Browser https://code.bioconductor.org/browse/bacon/
Package Short Url https://bioconductor.org/packages/bacon/
Package Downloads Report Download Stats