zenith
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().
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 |
| Downloads rank | 525 |
| Source branch | devel |
| biocViews | BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics |
Documentation
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 |
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