zenith

DOI: 10.18129/B9.bioc.zenith    

This is the development version of zenith; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.16)

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 "4.2") 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")

 

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 0.99.12
In Bioconductor since BioC 3.16 (R-4.2)
License Artistic-2.0
Depends R (>= 4.2.0), methods
Imports variancePartition(>= 1.26.0), limma, 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
Links To Me
Build Report  

Package Archives

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

Source Package zenith_0.99.12.tar.gz
Windows Binary zenith_0.99.12.zip
macOS Binary (x86_64) zenith_0.99.12.tgz
macOS Binary (arm64) zenith_0.99.12.tgz
Source Repository git clone https://git.bioconductor.org/packages/zenith
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/zenith
Package Short Url https://bioconductor.org/packages/zenith/
Package Downloads Report Download Stats

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