bacon
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see bacon.
Controlling bias and inflation in association studies using the empirical null distribution
Bioconductor version: 3.9
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 "3.6") 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 | 1.12.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 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_1.12.0.tar.gz |
| Windows Binary | bacon_1.12.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | bacon_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/bacon |
| Source Repository (Developer Access) | git clone [email protected]:packages/bacon |
| Bioc Package Browser | https://code.bioconductor.org/browse/bacon/ |
| Package Short Url | https://bioconductor.org/packages/bacon/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |