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("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 | R Script | |
2) Additional visualizations | R Script | |
3) Theory and practice of random effects | R Script | |
4) Differential expression testing with repeated measures designs | HTML | R Script |
Reference Manual | ||
NEWS | Text |
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 |
See More
Suggests | BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
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 |