variancePartition

This package is for version 3.7 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: 3.7

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 "3.5") 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) Tutorial on using variancePartition PDF R Script

2) Additional visualizations PDF R Script

3) Theory and practice of random effects PDF R Script

4) Differential expression testing with repeated measures designs HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, DifferentialExpression, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcription

Version 1.10.4

In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)

License GPL (>= 2)

Depends R (>= 3.0.0), ggplot2, limma, foreach, scales, Biobase, methods

Imports MASS, pbkrtest (>= 0.4-4), lmerTest, iterators, splines, colorRamps, gplots, reshape2, lme4 (>= 1.1-10), doParallel, grDevices, graphics, utils, stats

System Requirements

URL

Suggests BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr

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Package Archives

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

Source Package variancePartition_1.10.4.tar.gz

Windows Binary variancePartition_1.10.4.zip

Mac OS X 10.11 (El Capitan) variancePartition_1.10.4.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 3.7 Source Archive