bacon
Controlling bias and inflation in association studies using the empirical null distribution
Bioconductor version: Release (3.19)
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("bacon")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
NEWS | Text |
Details
biocViews | BatchEffect, Bayesian, GenomeWideAssociation, ImmunoOncology, MethylationArray, MultipleComparison, RNASeq, Regression, Software, StatisticalMethod, Transcriptomics |
Version | 1.32.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (8.5 years) |
License | GPL (>= 2) |
Depends | R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse |
Imports | |
System Requirements | |
URL |
See More
Suggests | BiocStyle, knitr, rmarkdown, testthat, roxygen2 |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | bacon_1.32.0.tar.gz |
Windows Binary | bacon_1.32.0.zip (64-bit only) |
macOS Binary (x86_64) | bacon_1.32.0.tgz |
macOS Binary (arm64) | bacon_1.32.0.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 |