Package: mariner
Type: Package
Title: Mariner: Explore the Hi-Cs
Version: 1.10.0
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: 7.3.2
Depends: R (>= 4.2.0)
Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub,
        marinerData, TxDb.Hsapiens.UCSC.hg38.knownGene, fields
Imports: methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges,
        InteractionSet, data.table, stats, rlang, glue, assertthat,
        plyranges, 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
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:23:11 UTC
RemoteUrl: https://github.com/bioc/mariner
RemoteRef: RELEASE_3_22
RemoteSha: 0e27ac7477787086d76f90318f41d1f8cf5cbcdc
NeedsCompilation: no
Packaged: 2025-11-11 15:51:58 UTC; root
Author: Eric Davis [aut, cre] (ORCID: <https://orcid.org/0000-0003-4051-3217>),
  Sarah Parker [aut] (ORCID: <https://orcid.org/0000-0002-2700-3979>)
Maintainer: Eric Davis <ericscottdavis@outlook.com>
Built: R 4.5.2; ; 2025-11-12 03:00:03 UTC; windows
