Bioconductor - zenith

Bioconductor - zenith
Bioconductor 3.22
Software Packages
zenith
zenith
This is the
released
version of zenith; for the devel version, see
zenith
Gene set analysis following differential expression using linear (mixed) modeling with dream
DOI:
10.18129/B9.bioc.zenith
Bioconductor version:
Release (3.22)
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]
ORCID: 0000-0002-0957-0224
Maintainer:
Gabriel Hoffman
Citation (from within R, enter
citation("zenith")
):
Installation
To install this package, start R (version "4.5") 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
PDF
NEWS
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
BatchEffect
DifferentialExpression
Epigenetics
FunctionalGenomics
GeneExpression
GeneSetEnrichment
ImmunoOncology
Microarray
Normalization
Preprocessing
QualityControl
RNASeq
Regression
Software
Transcriptomics
Version
1.12.0
In Bioconductor since
BioC 3.16 (R-4.2) (3.5 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
Rfast
ggplot2
tidyr
dplyr
reshape2
progress
, utils,
Rdpack
, stats
System Requirements
URL
Bug Reports
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
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Installation
instructions to use this package in your R session.
Source Package
zenith_1.12.0.tar.gz
Windows Binary (x86_64)
zenith_1.12.0.zip
(64-bit only)
macOS Binary (x86_64)
zenith_1.12.0.tgz
macOS Binary (arm64)
zenith_1.12.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/zenith
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/zenith
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