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Bioconductor - variancePartition

variancePartition

This is the released version of variancePartition; for the devel version, see variancePartition.

Quantify and interpret drivers of variation in multilevel gene expression experiments

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-0957-0224

Maintainer: Gabriel E. Hoffman <gabriel.hoffman at mssm.edu>

Citation (from within R, enter citation("variancePartition")): Installation

To install this package, start R (version "4.5") 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")

Details biocViews BatchEffect, DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, Normalization, Preprocessing, QualityControl, RNASeq, Regression, Software, Transcriptomics Version 1.38.0 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.

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