zenith

DOI: 10.18129/B9.bioc.zenith  

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

Bioconductor version: Release (3.17)

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")

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")

 

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

Details

biocViews	BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version	1.2.0
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
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
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_1.2.0.tar.gz
Windows Binary	zenith_1.2.0.zip
macOS Binary (x86_64)	zenith_1.2.0.tgz
macOS Binary (arm64)	zenith_1.2.0.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
Old Source Packages for BioC 3.17	Source Archive