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 (3.24)
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("bacon")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text |
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 |
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_1.41.0.tar.gz |
| Windows Binary (x86_64) | bacon_1.41.0.zip |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/bacon/ |
| Package Short Url | https://bioconductor.org/packages/bacon/ |
| Package Downloads Report | Download Stats |