variancePartition

This is the development version of variancePartition; for the stable release version, see variancePartition.

Quantify and interpret drivers of variation in multilevel gene expression experiments

Bioconductor version: Development (3.23)

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: 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 "4.6") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.41.3
In Bioconductor since	BioC 3.2 (R-3.2) (10.5 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, reformulas, matrixStats, RhpcBLASctl, reformulas, 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
Build Report	Build Report

Package Archives

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

Source Package	variancePartition_1.41.3.tar.gz
Windows Binary (x86_64)	variancePartition_1.41.3.zip
macOS Binary (big-sur-x86_64)	variancePartition_1.41.3.tgz
macOS Binary (big-sur-arm64)	variancePartition_1.41.2.tgz
macOS Binary (sonoma-arm64)	variancePartition_1.41.3.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