variancePartition

DOI: 10.18129/B9.bioc.variancePartition    

This is the development version of variancePartition; for the stable release version, see variancePartition.

Quantify and interpret divers of variation in multilevel gene expression experiments

Bioconductor version: Development (3.15)

Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures.

Author: Gabriel Hoffman [aut, cre]

Maintainer: Gabriel E. Hoffman <gabriel.hoffman at mssm.edu>

Citation (from within R, enter citation("variancePartition")):

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("variancePartition")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version 1.25.0
In Bioconductor since BioC 3.2 (R-3.2) (6 years)
License GPL (>= 2)
Depends R (>= 4.0.0), ggplot2, limma, BiocParallel
Imports MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix, iterators, foreach, doParallel, gplots, progress, reshape2, scales, rlang, lme4 (>= 1.1-10), grDevices, graphics, Biobase, methods, utils, stats
LinkingTo
Suggests BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr
SystemRequirements
Enhances
URL http://bioconductor.org/packages/variancePartition https://github.com/GabrielHoffman/variancePartition
BugReports https://github.com/GabrielHoffman/variancePartition/issues
Depends On Me
Imports Me muscat
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/variancePartition
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/variancePartition
Package Short Url https://bioconductor.org/packages/variancePartition/
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