DESCRIPTION

Package: variancePartition
Type: Package
Title: Quantify and interpret drivers of variation in multilevel gene expression experiments
Version: 1.36.3
Date: 2025-01-02
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 (>= 3.62.1),
    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
RoxygenNote: 7.3.2
RdMacros: Rdpack