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Bioconductor - bacon (development version)

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 (3.22)

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 "4.5") 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 1.37.0 In Bioconductor since BioC 3.3 (R-3.3) (9 years) License GPL (>= 2) Depends R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Imports System Requirements URL See More Package Archives

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

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