Package: mariner
Type: Package
Title: Mariner: Explore the Hi-Cs
Version: 1.6.0
Authors@R: c(
    person("Eric", "Davis", role = c("aut", "cre"),
      email = "ericscottdavis@outlook.com",
      comment = c(ORCID = "0000-0003-4051-3217"))
  )
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: 7.2.3
Depends: R (>= 4.2.0)
Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub,
        marinerData
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: GPL-3
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-InteractionMatrix.R'
        'methods-MatrixSelection.R' 'methods-MergedGInteractions.R'
        'methods-adjustEnrichment.R' 'methods-aggHicMatrices.R'
        'methods-as_ginteractions.R' 'methods-binPairs.R'
        'methods-binRanges.R' 'methods-calcLoopEnrichment.R'
        'methods-changePixelRes.R' 'methods-hdf5BlockApply.R'
        'methods-mergePairs.R' 'methods-pixelsToMatrices.R'
        'methods-plotBullseye.R' 'methods-plotMatrix.R'
        'methods-pullHic.R' 'methods-removeShortPairs.R'
        'methods-shiftRanges.R' 'methods-snapToBins.R' 'zzz.R'
URL: http://ericscottdavis.com/mariner/
git_url: https://git.bioconductor.org/packages/mariner
git_branch: RELEASE_3_20
git_last_commit: 1aa9d93
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: no
Packaged: 2024-10-30 01:25:38 UTC; biocbuild
Author: Eric Davis [aut, cre] (<https://orcid.org/0000-0003-4051-3217>)
Maintainer: Eric Davis <ericscottdavis@outlook.com>
Built: R 4.4.2; ; 2025-01-01 00:29:17 UTC; unix
