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Gene set analysis following differential expression using linear (mixed) modeling with dream

Bioconductor version: Release (3.19)

Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method from the limma package proposed by Wu and Smyth (2012). Zenith is a simple extension of camera to be compatible with linear mixed models implemented in variancePartition::dream().

Author: Gabriel Hoffman [aut, cre]

Maintainer: Gabriel Hoffman <gabriel.hoffman at>

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


To install this package, start R (version "4.4") 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:

Example usage of zenith on GEUVAIDIS RNA-seq HTML R Script
Example usage of zenith on RNA-seq HTML R Script
Reference Manual PDF


biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2.0), limma, methods
Imports variancePartition(>= 1.26.0), EnrichmentBrowser(>= 2.22.0), GSEABase(>= 1.54.0), msigdbr (>= 7.5.1), Rfast, ggplot2, tidyr, reshape2, progress, utils, Rdpack, stats
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Suggests BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit
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Depends On Me
Imports Me dreamlet
Suggests Me variancePartition
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Follow Installation instructions to use this package in your R session.

Source Package zenith_1.6.0.tar.gz
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macOS Binary (x86_64) zenith_1.6.0.tgz
macOS Binary (arm64) zenith_1.6.0.tgz
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