Package: mariner
Type: Package
Title: Mariner: Explore the Hi-Cs
Version: 1.11.1
Authors@R: c(
    person("Eric", "Davis", role = c("aut", "cre"),
      email = "ericscottdavis@outlook.com",
      comment = c(ORCID = "0000-0003-4051-3217")),
    person("Sarah", "Parker", role = c("aut"),
      email = "smp3800@gmail.com",
      comment = c(ORCID = "0000-0002-2700-3979"))
  )
Description: Tools for manipulating paired ranges and
    working with Hi-C data in R. Functionality includes
    manipulating/merging paired regions, generating
    paired ranges, extracting/aggregating interactions
    from `.hic` files, and visualizing the results. 
    Designed for compatibility with plotgardener for
    visualization.
RoxygenNote: 7.3.3
Depends: R (>= 4.2.0)
Suggests:
    knitr,
    testthat (>= 3.0.0),
    rmarkdown,
    ExperimentHub,
    marinerData,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    fields
Imports:
    methods,
    S4Vectors,
    BiocGenerics,
    BiocManager,
    GenomicRanges,
    InteractionSet,
    data.table,
    stats,
    rlang,
    glue,
    assertthat,
    dplyr,
    magrittr,
    dbscan,
    purrr,
    progress,
    GenomeInfoDb,
    strawr (>= 0.0.91),
    DelayedArray,
    HDF5Array,
    abind,
    BiocParallel,
    IRanges,
    SummarizedExperiment,
    rhdf5,
    plotgardener,
    RColorBrewer,
    colourvalues,
    utils,
    grDevices,
    graphics,
    grid
biocViews:
    FunctionalGenomics,
    Visualization,
    HiC
VignetteBuilder: knitr
License: MIT + file LICENSE
Encoding: UTF-8
Config/testthat/edition: 3
Collate: 
    'AllClasses.R'
    'AllGenerics.R'
    'mariner.R'
    'methods-CountMatrix.R'
    'methods-GInteractions.R'
    'utils.R'
    'methods-InteractionArray.R'
    'methods-InteractionJaggedArray.R'
    'methods-InteractionMatrix.R'
    'methods-JaggedArray.R'
    'methods-MatrixSelection.R'
    'methods-MergedGInteractions.R'
    'methods-adjustEnrichment.R'
    'methods-aggHicMatrices.R'
    'methods-as_ginteractions.R'
    'methods-assignToBins.R'
    'methods-binRanges.R'
    'methods-calcLoopEnrichment.R'
    'methods-changePixelRes.R'
    'methods-hdf5BlockApply.R'
    'methods-makeRandomGInteractions.R'
    'methods-mergePairs.R'
    'methods-pileupBoundaries.R'
    'methods-pileupDomains.R'
    'methods-pileupPixels.R'
    'methods-pixelsToMatrices.R'
    'methods-plotBullseye.R'
    'methods-plotMatrix.R'
    'methods-pullHic.R'
    'methods-regularize.R'
    'methods-removeShortPairs.R'
    'methods-shiftRanges.R'
    'methods-snapToBins.R'
    'zzz.R'
URL: 
    https://ericscottdavis.com/mariner/,
    https://github.com/EricSDavis/mariner
git_url: https://git.bioconductor.org/packages/mariner
git_branch: devel
git_last_commit: 84a2021
git_last_commit_date: 2025-11-29
Repository: Bioconductor 3.23
