BADER
This is the development version of BADER; for the stable release version, see BADER.
Bayesian Analysis of Differential Expression in RNA Sequencing Data
Bioconductor version: Development (3.24)
For RNA sequencing count data, BADER fits a Bayesian hierarchical model. The algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.
Author: Andreas Neudecker, Matthias Katzfuss
Maintainer: Andreas Neudecker <a.neudecker at arcor.de>
citation("BADER")):
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("BADER")
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("BADER")| Analysing RNA-Seq data with the "BADER" package | R Script | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, ImmunoOncology, RNASeq, SAGE, Sequencing, Software |
| Version | 1.51.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 years) |
| License | GPL-2 |
| Depends | |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | pasilla(>= 0.2.10) |
| 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 | BADER_1.51.0.tar.gz |
| Windows Binary (x86_64) | BADER_1.51.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | BADER_1.51.0.tgz |
| macOS Binary (sonoma-arm64) | BADER_1.51.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BADER |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BADER |
| Bioc Package Browser | https://code.bioconductor.org/browse/BADER/ |
| Package Short Url | https://bioconductor.org/packages/BADER/ |
| Package Downloads Report | Download Stats |