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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see baySeq.

Empirical Bayesian analysis of patterns of differential expression in count data

Bioconductor version: Release (3.18)

This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

Author: Thomas J. Hardcastle

Maintainer: Thomas J. Hardcastle <tjh48 at cam.ac.uk>

Citation (from within R, enter citation("baySeq")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Advanced baySeq analyses PDF R Script
baySeq PDF R Script
Reference Manual PDF


biocViews DifferentialExpression, MultipleComparison, SAGE, Sequencing, Software
Version 2.36.0
In Bioconductor since BioC 2.5 (R-2.10) (14.5 years)
License GPL-3
Depends R (>= 2.3.0), methods, GenomicRanges, abind, parallel
Imports edgeR
System Requirements
See More
Suggests BiocStyle, BiocGenerics
Linking To
Depends On Me clusterSeq, segmentSeq, TCC
Imports Me riboSeqR, srnadiff
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package baySeq_2.36.0.tar.gz
Windows Binary baySeq_2.36.0.zip
macOS Binary (x86_64) baySeq_2.36.0.tgz
macOS Binary (arm64) baySeq_2.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/baySeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/baySeq
Package Short Url https://bioconductor.org/packages/baySeq/
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