variancePartition

This is the released version of variancePartition; for the devel version, see variancePartition.

Quantify and interpret drivers of variation in multilevel gene expression experiments

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DOI: 10.18129/B9.bioc.variancePartition

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0002-0957-0224

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

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics

Version 1.40.0

In Bioconductor since BioC 3.2 (R-3.2) (10 years)

License GPL-2

Depends R (>= 4.3.0), ggplot2, limma(>= 3.62.2), BiocParallel

Imports MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, gtools, 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

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 crumblr, muscat, zenith

Suggests Me GRaNIE

Links To Me

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Package Archives

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

Source Package variancePartition_1.40.0.tar.gz

Windows Binary (x86_64) variancePartition_1.40.0.zip

macOS Binary (x86_64) variancePartition_1.40.0.tgz

macOS Binary (arm64) variancePartition_1.40.0.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/

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