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: 1.37.1
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 (>= 3.5.0), 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: 7987c50
git_last_commit_date: 2025-06-27
Repository: Bioconductor 3.22
Date/Publication: 2025-06-27
NeedsCompilation: no
Packaged: 2025-06-28 00:28:29 UTC; biocbuild
Author: Gabriele Schweikert [cre, aut],
  David Kuo [aut]
Maintainer: Gabriele Schweikert <gschweik@staffmail.ed.ac.uk>
Built: R 4.5.1; ; 2025-06-28 13:10:50 UTC; windows
