Package: zenith
Type: Package
Title: Gene set analysis following differential expression using linear
        (mixed) modeling with dream
Version: 1.11.0
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
git_url: https://git.bioconductor.org/packages/zenith
git_branch: devel
git_last_commit: 3dbfcb4
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 02:53:29 UTC; biocbuild
Author: Gabriel Hoffman [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0957-0224>)
Maintainer: Gabriel Hoffman <gabriel.hoffman@mssm.edu>
Built: R 4.5.0; ; 2025-06-05 14:19:43 UTC; windows
