variancePartition

DOI: 10.18129/B9.bioc.variancePartition    

This is the development version of variancePartition; to use it, please install the devel version of Bioconductor.

Quantify and interpret divers of variation in multilevel gene expression experiments

Bioconductor version: Development (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 (!requireNamespace("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")

 

PDF R Script 1) Tutorial on using variancePartition
HTML R Script 2) Additional visualizations
PDF R Script 3) Theory and practice of random effects
HTML R Script 4) dream: differential expression testing with repeated measures designs
PDF   Reference Manual
Text   NEWS

Details

biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics
Version 1.15.8
In Bioconductor since BioC 3.2 (R-3.2) (4 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
LinkingTo
Suggests BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr
SystemRequirements
Enhances
URL
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_1.15.8.tar.gz
Windows Binary variancePartition_1.15.8.zip
Mac OS X 10.11 (El Capitan) variancePartition_1.15.8.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

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