bacon

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

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

Bioconductor version: Development (3.24)

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")):

Maarten van Iterson. bacon: Controlling bias and inflation in association studies using the empirical null distribution. doi:10.18129/B9.bioc.bacon, R package version 1.41.0, https://bioconductor.org/packages/bacon.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BatchEffect, Bayesian, GenomeWideAssociation, ImmunoOncology, MethylationArray, MultipleComparison, RNASeq, Regression, Software, StatisticalMethod, Transcriptomics
Version	1.41.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	GPL (>= 2)
Depends	R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse
Imports
System Requirements
URL

Suggests	BiocStyle, knitr, rmarkdown, testthat, roxygen2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	bacon_1.41.0.tar.gz
Windows Binary (x86_64)	bacon_1.41.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	bacon_1.41.0.tgz
macOS Binary (sonoma-arm64)	bacon_1.41.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/bacon
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bacon
Package Short Url	https://bioconductor.org/packages/bacon/
Package Downloads Report	Download Stats