Package: zenith
Type: Package
Title: Gene set analysis following differential expression using linear
        (mixed) modeling with dream
Version: 1.15.0
Date: 2025-04-03
Authors@R: person("Gabriel", "Hoffman", role=c("aut", "cre"), email="gabriel.hoffman@mssm.edu", comment=c(ORCID="0000-0002-0957-0224"))
Description: 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().
VignetteBuilder: knitr
License: Artistic-2.0
Encoding: UTF-8
URL: https://DiseaseNeuroGenomics.github.io/zenith
BugReports: https://github.com/DiseaseNeuroGenomics/zenith/issues
Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown,
        tweeDEseqCountData, edgeR, kableExtra, RUnit
biocViews: RNASeq, GeneExpression, GeneSetEnrichment,
        DifferentialExpression, BatchEffect, QualityControl,
        Regression, Epigenetics, FunctionalGenomics, Transcriptomics,
        Normalization, Preprocessing, Microarray, ImmunoOncology,
        Software
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
RdMacros: Rdpack
RoxygenNote: 7.3.2
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libxml2-dev
        libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:58:49 UTC
RemoteUrl: https://github.com/bioc/zenith
RemoteRef: HEAD
RemoteSha: a5f57fabb9cb1488e12c980b8fb3531f0549fbc3
NeedsCompilation: no
Packaged: 2026-07-03 23:55:40 UTC; root
Author: Gabriel Hoffman [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0957-0224>)
Maintainer: Gabriel Hoffman <gabriel.hoffman@mssm.edu>