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 (3.18)

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 "4.3") 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	1.3.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
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
Linking To
Suggests	BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit
System Requirements
Enhances
URL	https://DiseaseNeuroGenomics.github.io/zenith
Bug Reports	https://github.com/DiseaseNeuroGenomics/zenith/issues

Depends On Me
Imports Me
Suggests Me	variancePartition
Links To Me
Build Report

Package Archives

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

Source Package	zenith_1.3.0.tar.gz
Windows Binary	zenith_1.3.0.zip
macOS Binary (x86_64)	zenith_1.3.0.tgz
macOS Binary (arm64)	zenith_1.3.0.tgz
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