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variancePartition

Quantify and interpret drivers of variation in multilevel gene expression experiments


Bioconductor version: Release (3.18)

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 "4.3") and enter:


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

BiocManager::install("variancePartition")

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("variancePartition")
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
NEWS Text

Details

biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version 1.32.5
In Bioconductor since BioC 3.2 (R-3.2) (8.5 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
System Requirements
URL http://bioconductor.org/packages/variancePartition https://DiseaseNeuroGenomics.github.io/variancePartition
Bug Reports https://github.com/DiseaseNeuroGenomics/variancePartition/issues
See More
Suggests BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr
Linking To
Enhances
Depends On Me dreamlet
Imports Me muscat, zenith
Suggests Me GRaNIE
Links To Me
Build Report Build Report

Package Archives

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

Source Package variancePartition_1.32.5.tar.gz
Windows Binary variancePartition_1.32.5.zip (64-bit only)
macOS Binary (x86_64) variancePartition_1.32.5.tgz
macOS Binary (arm64) variancePartition_1.32.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/variancePartition
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/variancePartition
Bioc Package Browser https://code.bioconductor.org/browse/variancePartition/
Package Short Url https://bioconductor.org/packages/variancePartition/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive