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 (>= 3.5.0), 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'
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:32:14 UTC
RemoteUrl: https://github.com/bioc/MMDiff2
RemoteRef: HEAD
RemoteSha: d528d04d4ba1f53144fb922eaad4b6296c3c8045
NeedsCompilation: no
Packaged: 2026-03-17 09:22:39 UTC; root
Author: Gabriele Schweikert [cre, aut],
  David Kuo [aut]
Maintainer: Gabriele Schweikert <gschweik@staffmail.ed.ac.uk>
Built: R 4.6.0; ; 2026-03-17 09:26:41 UTC; windows
