zenith
Gene set analysis following differential expression using linear (mixed) modeling with dream
Bioconductor version: 3.23 · Package version: 1.14.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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().
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("zenith")Details
| Maintainer | Gabriel Hoffman <gabriel.hoffman@mssm.edu> |
| Author | Gabriel Hoffman [aut, cre] (ORCID: <https://orcid.org/0000-0002-0957-0224>) |
| License | Artistic-2.0 |
| URL | https://DiseaseNeuroGenomics.github.io/zenith |
| Bug Reports | https://github.com/DiseaseNeuroGenomics/zenith/issues |
| Source branch | RELEASE_3_23 |
| 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/ |
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 1.14.0, https://bioconductor.org/packages/zenith.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | zenith_1.14.0.tar.gz |
| Windows binary (x86_64) | zenith_1.14.0.zip |
| macOS binary (arm64) | zenith_1.14.0.tgz |
| macOS binary (x86_64) | zenith_1.14.0.tgz |
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