variancePartition

DOI: 10.18129/B9.bioc.variancePartition    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see variancePartition.

Quantify and interpret divers of variation in multilevel gene expression experiments

Bioconductor version: 3.11

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 E. Hoffman

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF	R Script	1) Tutorial on using variancePartition
HTML	R Script	2) Additional visualizations
PDF	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

Details

biocViews	BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version	1.18.3
In Bioconductor since	BioC 3.2 (R-3.2) (5 years)
License	GPL (>= 2)
Depends	R (>= 3.6.0), ggplot2, limma, foreach, scales, Biobase, methods
Imports	MASS, pbkrtest (>= 0.4-4), lmerTest, iterators, splines, colorRamps, BiocParallel, gplots, progress, reshape2, lme4 (>= 1.1-10), doParallel, grDevices, graphics, utils, stats
LinkingTo
Suggests	BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr
SystemRequirements
Enhances
URL
BugReports	https://github.com/GabrielHoffman/variancePartition/issues
Depends On Me
Imports Me	BioMM, muscat
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	variancePartition_1.18.3.tar.gz
Windows Binary	variancePartition_1.18.3.zip
macOS 10.13 (High Sierra)	variancePartition_1.18.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/variancePartition
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/variancePartition
Package Short Url	https://bioconductor.org/packages/variancePartition/
Package Downloads Report	Download Stats