DOI: 10.18129/B9.bioc.variancePartition    

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

Quantify and interpret divers of variation in multilevel gene expression experiments

Bioconductor version: Development (3.10)

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 E. Hoffman

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

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script 1) Tutorial on using variancePartition
HTML R Script 2) Additional visualizations
PDF R Script 3) Theory and practice of random effects
HTML R Script 4) dream: differential expression testing with repeated measures designs
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version 1.15.8
In Bioconductor since BioC 3.2 (R-3.2) (4 years)
License GPL (>= 2)
Depends R (>= 3.5.0), ggplot2, limma, foreach, scales, Biobase, methods
Imports MASS, pbkrtest (>= 0.4-4), lmerTest, iterators, splines, colorRamps, BiocParallel, gplots, progress, reshape2, lme4 (>= 1.1-10), doParallel, grDevices, graphics, utils, stats
Suggests BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr
Depends On Me
Imports Me BioMM, muscat
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package variancePartition_1.15.8.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) variancePartition_1.15.8.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: