variancePartition

DOI: 10.18129/B9.bioc.variancePartition    

Quantify and interpret divers of variation in multilevel gene expression experiments

Bioconductor version: Release (3.15)

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]

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

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

Installation

To install this package, start R (version "4.2") 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")

 

PDF R Script 1) Tutorial on using variancePartition
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) 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 1.26.0
In Bioconductor since BioC 3.2 (R-3.2) (7 years)
License GPL-2
Depends R (>= 4.0.0), ggplot2, limma, BiocParallel
Imports MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix, iterators, foreach, doParallel, gplots, RhpcBLASctl, progress, reshape2, aod, scales, Rdpack, rlang, lme4 (>= 1.1-10), grDevices, graphics, Biobase, methods, utils, stats
LinkingTo
Suggests BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr
SystemRequirements
Enhances
URL http://bioconductor.org/packages/variancePartition https://DiseaseNeuroGenomics.github.io/variancePartition
BugReports https://github.com/DiseaseNeuroGenomics/variancePartition/issues
Depends On Me
Imports Me muscat
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package variancePartition_1.26.0.tar.gz
Windows Binary variancePartition_1.26.0.zip (64-bit only)
macOS Binary (x86_64) variancePartition_1.26.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: