DOI: 10.18129/B9.bioc.variancePartition  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see variancePartition.

Quantify and interpret drivers of variation in multilevel gene expression experiments

Bioconductor version: 3.16

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")):


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PDF R Script 1) Tutorial on using variancePartition
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) Frequently asked questions
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version 1.28.9
In Bioconductor since BioC 3.2 (R-3.2) (7.5 years)
License GPL-2
Depends R (>= 4.0.0), ggplot2, limma, BiocParallel
Imports MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, foreach, doParallel, gplots, RhpcBLASctl, progress, reshape2, remaCor (>= 0.0.11), aod, scales, Rdpack, rlang, lme4 (>= 1.1-10), grDevices, graphics, Biobase, methods, utils, stats
Suggests BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr
Depends On Me
Imports Me muscat, zenith
Suggests Me GRaNIE
Links To Me
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