zenith

DOI: 10.18129/B9.bioc.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>

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

PDF		Reference Manual

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) (0.5 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
LinkingTo
Suggests	BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit
SystemRequirements
Enhances
URL	https://DiseaseNeuroGenomics.github.io/zenith
BugReports	https://github.com/DiseaseNeuroGenomics/zenith/issues
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Build Report

Package Archives

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

Source Package
Windows Binary	zenith_1.3.0.zip
macOS Binary (x86_64)	zenith_1.3.0.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