variancePartition

This package is for version 3.10 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: 3.10

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>

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

Installation

To install this package, start R (version "3.6") 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) Tutorial on using variancePartition PDF R Script
2) Additional visualizations HTML R Script
3) Theory and practice of random effects PDF R Script
4) dream: differential expression testing with repeated measures designs 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 1.16.1
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL (>= 2)
Depends R (>= 3.5.0), 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
System Requirements
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Suggests BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr
Linking To
Enhances
Depends On Me
Imports Me BioMM, muscat
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package variancePartition_1.16.1.tar.gz
Windows Binary variancePartition_1.16.1.zip
Mac OS X 10.11 (El Capitan) variancePartition_1.16.1.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 3.10 Source Archive