variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experiments
Bioconductor version: Release (3.19)
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("variancePartition")
):
Installation
To install this package, start R (version "4.4") 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) Variance partitioning analysis | 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) Error handling | HTML | R Script |
6) Frequently asked questions | HTML | R Script |
7) Multivariate tests | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics |
Version | 1.34.0 |
In Bioconductor since | BioC 3.2 (R-3.2) (9 years) |
License | GPL-2 |
Depends | R (>= 4.3.0), ggplot2, limma, BiocParallel |
Imports | MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods, utils, stats |
System Requirements | |
URL | http://bioconductor.org/packages/variancePartition https://DiseaseNeuroGenomics.github.io/variancePartition |
Bug Reports | https://github.com/DiseaseNeuroGenomics/variancePartition/issues |
See More
Suggests | BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr |
Linking To | |
Enhances | |
Depends On Me | dreamlet |
Imports Me | muscat, zenith |
Suggests Me | GRaNIE |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | variancePartition_1.34.0.tar.gz |
Windows Binary | variancePartition_1.34.0.zip |
macOS Binary (x86_64) | variancePartition_1.34.0.tgz |
macOS Binary (arm64) | variancePartition_1.34.0.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 |