BayesKnockdown
This is the released version of BayesKnockdown; for the devel version, see BayesKnockdown.
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
Bioconductor version: Release (3.23)
A simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. In the context of knockdown experiments, the predictor variable is the knocked-down gene, while the other genes are potential targets. Can also be used for differential expression/2-class data.
Author: William Chad Young
Maintainer: William Chad Young <wmchad at uw.edu>
citation("BayesKnockdown")):
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")
BiocManager::install("BayesKnockdown")
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("BayesKnockdown")| BayesKnockdown.pdf | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, GeneExpression, GeneTarget, Network, NetworkInference, Software |
| Version | 1.38.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | GPL-3 |
| Depends | R (>= 3.3) |
| Imports | stats, Biobase |
| System Requirements | |
| URL |
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| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BayesKnockdown_1.38.0.tar.gz |
| Windows Binary (x86_64) | BayesKnockdown_1.38.0.zip |
| macOS Binary (big-sur-x86_64) | BayesKnockdown_1.38.0.tgz |
| macOS Binary (sonoma-arm64) | BayesKnockdown_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BayesKnockdown |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BayesKnockdown |
| Bioc Package Browser | https://code.bioconductor.org/browse/BayesKnockdown/ |
| Package Short Url | https://bioconductor.org/packages/BayesKnockdown/ |
| Package Downloads Report | Download Stats |