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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.43.1 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 years) |
| License | GPL-2 |
| Depends | R (>= 4.3.0), ggplot2, limma(>= 3.62.2), BiocParallel |
| Imports | MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, reformulas, matrixStats, RhpcBLASctl, reformulas, reshape2, gtools, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 2.0-1), 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, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr |
| Linking To | |
| Enhances | |
| Depends On Me | dreamlet |
| Imports Me | crumblr, LimROTS, 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_1.43.1.tar.gz |
| Windows Binary (x86_64) | variancePartition_1.43.1.zip |
| macOS Binary (big-sur-x86_64) | variancePartition_1.43.1.tgz |
| macOS Binary (sonoma-arm64) | variancePartition_1.43.1.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 |