zenith
This is the development version of zenith; for the stable release version, see zenith.
All Bioconductor versions of zenith
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16
Gene set analysis following differential expression using linear (mixed) modeling with dream
Bioconductor version: 3.24 · Package version: 1.15.0
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 mssm.edu>
Citation
From within R, enter citation("zenith"):
Gabriel Hoffman. zenith: Gene set analysis following differential expression using linear (mixed) modeling with dream. doi:10.18129/B9.bioc.zenith, R package version 1.15.0, https://bioconductor.org/packages/zenith.
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("zenith")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.15.0 |
| License | Artistic-2.0 |
| URL | https://DiseaseNeuroGenomics.github.io/zenith |
| Bug Reports | https://github.com/DiseaseNeuroGenomics/zenith/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 years) |
| Downloads rank | 1058 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/zenith/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("zenith")| Loading gene sets | HTML | R Script |
| Zenith gene set testing after dream analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | zenith_1.15.0.tar.gz |
| Windows binary (x86_64) | zenith_1.15.0.zip |
| macOS binary (arm64) | zenith_1.15.0.tgz |
| macOS binary (x86_64) | zenith_1.15.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/zenith |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/zenith |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.2.0), limma, methods
Imports: variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0), GSEABase (>= 1.54.0), msigdbr, Rfast, ggplot2, tidyr, dplyr, reshape2, progress, utils, Rdpack, stats
Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit