Package: CNVRanger
Version: 1.27.0
Title: Summarization and expression/phenotype association of CNV ranges
Authors@R: c(
    person("Ludwig", "Geistlinger", email = "ludwig.geistlinger@gmail.com",
    role = c("aut", "cre"), comment = c(ORCID = "0000-0002-2495-5464")),
    person("Vinicius Henrique", "da Silva", role = "aut"),
    person("Marcel", "Ramos",
    role = "ctb", comment = c(ORCID = "0000-0002-3242-0582")),
    person("Levi", "Waldron",
    role = "ctb", comment = c(ORCID = "0000-0003-2725-0694"))
  )
Depends: 
    GenomicRanges,
    RaggedExperiment
Imports: 
    BiocGenerics,
    BiocParallel,
    GDSArray,
    GenomeInfoDb,
    IRanges,
    S4Vectors,
    SNPRelate,
    SummarizedExperiment, 
    data.table, 
    edgeR,
    gdsfmt,
    grDevices,
    lattice,
    limma,
    methods,
    plyr,
    qqman, 
    rappdirs,
    reshape2,
    stats,
    utils
Suggests:
    AnnotationHub,
    BSgenome.Btaurus.UCSC.bosTau6.masked, 
    BiocStyle,
    ComplexHeatmap,
    Gviz,
    MultiAssayExperiment,
    TCGAutils,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    curatedTCGAData,
    ensembldb,
    grid,
    knitr,
    org.Hs.eg.db,
    regioneR,
    rmarkdown,
    statmod
Description: The CNVRanger package implements a comprehensive tool suite for CNV analysis.
    This includes functionality for summarizing individual CNV calls across a population,
    assessing overlap with functional genomic regions, and association analysis 
    with gene expression and quantitative phenotypes.
License: Artistic-2.0
BugReports: https://github.com/waldronlab/CNVRanger/issues
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: 
    CopyNumberVariation,
    DifferentialExpression,
    GeneExpression,
    GenomeWideAssociation,
    GenomicVariation,
    Microarray, 
    RNASeq,
    SNP 
RoxygenNote: 7.2.3
Date: 2025-05-08
git_url: https://git.bioconductor.org/packages/CNVRanger
git_branch: devel
git_last_commit: 16600ca
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
