variancePartition
This is the development version of variancePartition; for the stable release version, see variancePartition.
Quantify and interpret drivers of variation in multilevel gene expression experiments
Bioconductor version: Development (3.22)
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 "4.5") and enter:
if (!require("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")| 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 | 1.39.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (9.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.3.0), ggplot2, limma(>= 3.62.1), 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 | crumblr, 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_1.39.0.tar.gz |
| Windows Binary (x86_64) | variancePartition_1.39.0.zip |
| macOS Binary (x86_64) | variancePartition_1.39.0.tgz |
| macOS Binary (arm64) | variancePartition_1.39.0.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 |