variancePartition
This package is for version 3.6 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: 3.6
Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables.
Author: Gabriel E. Hoffman
Maintainer: Gabriel E. Hoffman <gabriel.hoffman at mssm.edu>
citation("variancePartition")):
Installation
To install this package, start R (version "3.4") 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 | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, RNASeq, Regression, Software |
| Version | 1.8.1 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | GPL (>= 2) |
| Depends | ggplot2, foreach, Biobase, methods |
| Imports | MASS, pbkrtest (>= 0.4-4), iterators, splines, colorRamps, gplots, reshape2, lme4 (>= 1.1-10), doParallel, limma, grDevices, graphics, utils, stats |
| System Requirements | |
| URL |
See More
| Suggests | edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, readr, knitr, BiocStyle |
| 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_1.8.1.tar.gz |
| Windows Binary | variancePartition_1.8.1.zip |
| Mac OS X 10.11 (El Capitan) | variancePartition_1.8.1.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 |
| Old Source Packages for BioC 3.6 | Source Archive |