zenith
Gene set analysis following differential expression using linear (mixed) modeling with dream
Bioconductor version: Release (3.19)
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("zenith")):
Installation
To install this package, start R (version "4.4") 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")| Example usage of zenith on GEUVAIDIS RNA-seq | HTML | R Script |
| Example usage of zenith on RNA-seq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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 |
| System Requirements | |
| URL | https://DiseaseNeuroGenomics.github.io/zenith |
| Bug Reports | https://github.com/DiseaseNeuroGenomics/zenith/issues |
See More
| Suggests | BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | dreamlet |
| Suggests Me | variancePartition |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | zenith_1.6.0.tar.gz |
| Windows Binary (x86_64) | zenith_1.6.0.zip (64-bit only) |
| macOS Binary (x86_64) | zenith_1.6.0.tgz |
| macOS Binary (arm64) | zenith_1.6.0.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 |