DOI: 10.18129/B9.bioc.zenith  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see zenith.

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

Bioconductor version: 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>

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HTML R Script Example usage of zenith on GEUVAIDIS RNA-seq
HTML R Script Example usage of zenith on RNA-seq
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biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version 1.0.2
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
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
Suggests BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit
URL https://DiseaseNeuroGenomics.github.io/zenith
BugReports https://github.com/DiseaseNeuroGenomics/zenith/issues
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Source Package zenith_1.0.2.tar.gz
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