BADER

This is the released version of BADER; for the devel version, see BADER.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

Bayesian Analysis of Differential Expression in RNA Sequencing Data

Bioconductor version: Release (3.23)

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 (from within R, enter citation("BADER")):

Andreas Neudecker, Matthias Katzfuss. BADER: Bayesian Analysis of Differential Expression in RNA Sequencing Data. doi:10.18129/B9.bioc.BADER, R package version 1.50.0, https://bioconductor.org/packages/BADER.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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	PDF	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, ImmunoOncology, RNASeq, SAGE, Sequencing, Software
Version	1.50.0
In Bioconductor since	BioC 2.13 (R-3.0) (13 years)
License	GPL-2
Depends
Imports
System Requirements
URL

Suggests	pasilla (>= 0.2.10)
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Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	BADER_1.50.0.tar.gz
Windows Binary (x86_64)	BADER_1.50.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	BADER_1.50.0.tgz
macOS Binary (sonoma-arm64)	BADER_1.50.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BADER
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BADER
Package Short Url	https://bioconductor.org/packages/BADER/
Package Downloads Report	Download Stats