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Quantify and interpret drivers of variation in multilevel gene expression experiments

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

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


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:

1) Variance partitioning analysis HTML R Script
2) Additional visualizations HTML R Script
3) Theory and practice of random effects and REML HTML R Script
4) dream: differential expression testing with repeated measures designs HTML R Script
5) Error handling HTML R Script
6) Frequently asked questions HTML R Script
7) Multivariate tests HTML R Script
Reference Manual PDF


biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version 1.34.0
In Bioconductor since BioC 3.2 (R-3.2) (9 years)
License GPL-2
Depends R (>= 4.3.0), ggplot2, limma, BiocParallel
Imports MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods, utils, stats
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Suggests BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr
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Depends On Me dreamlet
Imports Me muscat, zenith
Suggests Me GRaNIE
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Follow Installation instructions to use this package in your R session.

Source Package variancePartition_1.34.0.tar.gz
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macOS Binary (x86_64) variancePartition_1.34.0.tgz
macOS Binary (arm64) variancePartition_1.34.0.tgz
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Source Repository (Developer Access) git clone
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