Package: variancePartition
Type: Package
Title: Quantify and interpret drivers of variation in multilevel gene
        expression experiments
Version: 1.40.1
Date: 2025-12-04
Authors@R: person("Gabriel", "Hoffman", role=c("aut", "cre"), email="gabriel.hoffman@mssm.edu", comment=c(ORCID="0000-0002-0957-0224"))
Maintainer: Gabriel E. Hoffman <gabriel.hoffman@mssm.edu>
Description: 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.
VignetteBuilder: knitr
License: GPL-2
Encoding: UTF-8
URL: http://bioconductor.org/packages/variancePartition,
        https://DiseaseNeuroGenomics.github.io/variancePartition
BugReports: https://github.com/DiseaseNeuroGenomics/variancePartition/issues
Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend,
        tximport, tximportData, ballgown, DESeq2, RUnit, cowplot,
        Rfast, zenith, statmod, BiocGenerics, r2glmm, readr
biocViews: RNASeq, GeneExpression, GeneSetEnrichment,
        DifferentialExpression, BatchEffect, QualityControl,
        Regression, Epigenetics, FunctionalGenomics, Transcriptomics,
        Normalization, Preprocessing, Microarray, ImmunoOncology,
        Software
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, reshape2, gtools, remaCor (>= 0.0.15), fANCOVA,
        aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices,
        graphics, Biobase, methods, utils, stats
RoxygenNote: 7.3.3
RdMacros: Rdpack
git_url: https://git.bioconductor.org/packages/variancePartition
git_branch: RELEASE_3_22
git_last_commit: ed3da37
git_last_commit_date: 2025-12-08
Repository: Bioconductor 3.22
Date/Publication: 2025-12-11
NeedsCompilation: no
Packaged: 2025-12-12 05:29:35 UTC; biocbuild
Author: Gabriel Hoffman [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0957-0224>)
Built: R 4.5.2; ; 2025-12-12 21:00:13 UTC; unix
