Package: MMDiff2
Description: This package detects statistically significant differences between
    read enrichment profiles in different ChIP-Seq samples. To take advantage of
    shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).
Type: Package
Title: Statistical Testing for ChIP-Seq data sets
Version: 1.39.0
Authors@R: c(
    person("Gabriele", "Schweikert", role = c("cre", "aut"), email = "gschweik@staffmail.ed.ac.uk"),
    person("David", "Kuo", role = "aut", email = "dkuo@cbio.mskcc.org"))
Depends:
    R (>= 3.3),
    Rsamtools,
    Biobase,
biocViews: ChIPSeq, DifferentialPeakCalling, Sequencing, Software
License: Artistic-2.0
Imports:
    GenomicRanges,
    locfit,
    BSgenome,
    Biostrings,
    shiny,
    ggplot2,
    RColorBrewer,
    graphics,
    grDevices,
    parallel,
    S4Vectors,
    methods
ImportFrom: utils txtProgressBar setTxtProgressBar read.csv
Suggests:
    MMDiffBamSubset,
    MotifDb,
    knitr,
    BiocStyle,
    BSgenome.Mmusculus.UCSC.mm9
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Collate:
    'DBAmmd-Class.R'
    'AllGenerics.R'
    'DBAmmd-Accessors.R'
    'DBAmmd-Showmethods.R'
    'DBAmmd-internal.R'
    'MMDiff2_data.R'
    'compDists.R'
    'compHists.R'
    'compPvals.R'
    'createPeakMatrix.R'
    'estimateFragmentCenters.R'
    'getPeakReads.R'
    'helperFcts.R'
    'plotDISTS4Peak.R'
    'plotDists.R'
    'plotPeak.R'
    'reportResults.R'
    'runShinyMMDiff2.R'
    'server.R'
    'ui.R'
git_url: https://git.bioconductor.org/packages/MMDiff2
git_branch: devel
git_last_commit: d528d04
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
