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zenith

This is the development version of zenith; for the stable release version, see zenith.

Gene set analysis following differential expression using linear (mixed) modeling with dream


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("zenith")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("zenith")
Example usage of zenith on GEUVAIDIS RNA-seq HTML R Script
Example usage of zenith on RNA-seq HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version 1.5.2
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2.0), limma, methods
Imports variancePartition(>= 1.26.0), EnrichmentBrowser(>= 2.22.0), GSEABase(>= 1.54.0), msigdbr (>= 7.5.1), Rfast, ggplot2, tidyr, reshape2, progress, utils, Rdpack, stats
System Requirements
URL https://DiseaseNeuroGenomics.github.io/zenith
Bug Reports https://github.com/DiseaseNeuroGenomics/zenith/issues
See More
Suggests BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit
Linking To
Enhances
Depends On Me
Imports Me dreamlet
Suggests Me variancePartition
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package zenith_1.5.2.tar.gz
Windows Binary zenith_1.5.2.zip (64-bit only)
macOS Binary (x86_64) zenith_1.5.2.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/zenith
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/zenith
Bioc Package Browser https://code.bioconductor.org/browse/zenith/
Package Short Url https://bioconductor.org/packages/zenith/
Package Downloads Report Download Stats