{
  "_id": "6a2274f1cd65a98ecbd4a547",
  "Package": "mariner",
  "Type": "Package",
  "Title": "Mariner: Explore the Hi-Cs",
  "Version": "1.12.0",
  "Authors@R": "c(\nperson(\"Eric\", \"Davis\", role = c(\"aut\", \"cre\"),\nemail = \"ericscottdavis@outlook.com\",\ncomment = c(ORCID = \"0000-0003-4051-3217\")),\nperson(\"Sarah\", \"Parker\", role = c(\"aut\"),\nemail = \"smp3800@gmail.com\",\ncomment = c(ORCID = \"0000-0002-2700-3979\"))\n)",
  "Description": "Tools for manipulating paired ranges and working with Hi-C\ndata in R. Functionality includes manipulating/merging paired\nregions, generating paired ranges, extracting/aggregating\ninteractions from `.hic` files, and visualizing the results.\nDesigned for compatibility with plotgardener for visualization.",
  "RoxygenNote": "7.3.3",
  "biocViews": "FunctionalGenomics, Visualization, HiC",
  "VignetteBuilder": "knitr",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Config/testthat/edition": "3",
  "Collate": "'AllClasses.R' 'AllGenerics.R' 'mariner.R'\n'methods-CountMatrix.R' 'methods-GInteractions.R' 'utils.R'\n'methods-InteractionArray.R' 'methods-InteractionJaggedArray.R'\n'methods-InteractionMatrix.R' 'methods-JaggedArray.R'\n'methods-MatrixSelection.R' 'methods-MergedGInteractions.R'\n'methods-adjustEnrichment.R' 'methods-aggHicMatrices.R'\n'methods-as_ginteractions.R' 'methods-assignToBins.R'\n'methods-binRanges.R' 'methods-calcLoopEnrichment.R'\n'methods-changePixelRes.R' 'methods-hdf5BlockApply.R'\n'methods-makeRandomGInteractions.R' 'methods-mergePairs.R'\n'methods-pileupBoundaries.R' 'methods-pileupDomains.R'\n'methods-pileupPixels.R' 'methods-pixelsToMatrices.R'\n'methods-plotBullseye.R' 'methods-plotMatrix.R'\n'methods-pullHic.R' 'methods-regularize.R'\n'methods-removeShortPairs.R' 'methods-shiftRanges.R'\n'methods-snapToBins.R' 'zzz.R'",
  "URL": "https://ericscottdavis.com/mariner/,\nhttps://github.com/EricSDavis/mariner",
  "Config/pak/sysreqs": "cmake make libbz2-dev liblzma-dev libuv1-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:00:45 UTC",
  "RemoteUrl": "https://github.com/bioc/mariner",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "212aa16d75088f8d81cd10a564c91cef524845c6",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-05 06:36:12 UTC",
    "User": "root"
  },
  "Author": "Eric Davis [aut, cre] (ORCID: <https://orcid.org/0000-0003-4051-3217>),\nSarah Parker [aut] (ORCID: <https://orcid.org/0000-0002-2700-3979>)",
  "Maintainer": "Eric Davis <ericscottdavis@outlook.com>",
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  "_created": "2026-06-05T06:36:12.000Z",
  "_published": "2026-06-05T07:04:17.343Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "login": "ericsdavis",
    "twitter": "@ericscottdavis1",
    "description": "Bioinformatics Scientist & Software Developer",
    "uuid": 31807001,
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    "visualization",
    "hic"
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  "_contributors": [
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ericsdavis/mariner",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "adjustEnrichment",
    "aggHicMatrices",
    "aggMetadata",
    "as_ginteractions",
    "as.list",
    "assignToBins",
    "binRanges",
    "calcLoopEnrichment",
    "cbind",
    "changePixelRes",
    "clusters",
    "colData",
    "countOverlaps",
    "counts",
    "counts<-",
    "defaultBuffer",
    "end1",
    "end2",
    "findOverlaps",
    "hdf5BlockApply",
    "InteractionArray",
    "InteractionJaggedArray",
    "InteractionMatrix",
    "interactions",
    "JaggedArray",
    "makeGInteractionsFromDataFrame",
    "makeRandomGInteractions",
    "makeRandomGRanges",
    "MatrixSelection",
    "MergedGInteractions",
    "mergePairs",
    "metadata",
    "overlapsAny",
    "path",
    "path<-",
    "pileupBoundaries",
    "pileupDomains",
    "pileupPixels",
    "pixelsToMatrices",
    "plotEnrichment",
    "plotMatrix",
    "pullHicMatrices",
    "pullHicPixels",
    "rbind",
    "regularize",
    "removeShortPairs",
    "selectBlock",
    "selectBottomLeft",
    "selectBottomRight",
    "selectCenterPixel",
    "selectCols",
    "selectCoordinates",
    "selectCorners",
    "selectInner",
    "selectionMethod",
    "selectOuter",
    "selectPixel",
    "selectRadius",
    "selectRows",
    "selectSubmatrix",
    "selectTopLeft",
    "selectTopRight",
    "seqnames1",
    "seqnames2",
    "sets",
    "shiftRanges",
    "show",
    "snapToBins",
    "sources",
    "start1",
    "start2",
    "subsetByOverlaps"
  ],
  "_help": [
    {
      "page": "mariner-package",
      "title": "Mariner: Explore the Hi-Cs",
      "topics": [
        "mariner-package",
        "mariner"
      ]
    },
    {
      "page": "aggHicMatrices",
      "title": "Aggregate count matrices from InteractionArray objects",
      "topics": [
        "aggHicMatrices",
        "aggHicMatrices,InteractionArray-method"
      ]
    },
    {
      "page": "aggMetadata",
      "title": "Aggregate the metadata columns of merged pairs",
      "topics": [
        "aggMetadata",
        "aggMetadata,MergedGInteractions,character,character_OR_function_OR_list-method"
      ]
    },
    {
      "page": "as_ginteractions",
      "title": "Convert DataFrames to GInteraction objects",
      "topics": [
        "as_ginteractions",
        "as_ginteractions,DF_OR_df_OR_dt,logical_OR_missing,logical_OR_missing-method",
        "makeGInteractionsFromDataFrame",
        "makeGInteractionsFromDataFrame,DF_OR_df_OR_dt,logical_OR_missing,logical_OR_missing-method"
      ]
    },
    {
      "page": "assignToBins",
      "title": "Flexibly bin paired ranges",
      "topics": [
        "assignToBins",
        "assignToBins,DF_OR_df_OR_dt,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method",
        "assignToBins,GInteractions,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method"
      ]
    },
    {
      "page": "binRanges",
      "title": "Flexibly bin ranges",
      "topics": [
        "binRanges",
        "binRanges,GRanges,numeric,character_OR_numeric_OR_missing-method"
      ]
    },
    {
      "page": "calcLoopEnrichment",
      "title": "Calculate loop enrichment over background.",
      "topics": [
        "calcLoopEnrichment",
        "calcLoopEnrichment,GInteractions,character-method",
        "calcLoopEnrichment,InteractionArray,missing-method"
      ]
    },
    {
      "page": "changePixelRes",
      "title": "Change pixels from one resolution to another selecting the new pixel using Hi-C data.",
      "topics": [
        "changePixelRes",
        "changePixelRes,GInteractions,character-method"
      ]
    },
    {
      "page": "clusters",
      "title": "Get clustered pairs from MergedGInteractions object",
      "topics": [
        "clusters",
        "clusters,MergedGInteractions-method"
      ]
    },
    {
      "page": "counts",
      "title": "Access count matrices from InteractionArray or InteractionMatrix",
      "topics": [
        "counts,InteractionArray-method",
        "counts,InteractionMatrix-method",
        "counts<-,InteractionMatrix-method"
      ]
    },
    {
      "page": "defaultBuffer",
      "title": "Return default buffer If InteractionArray is supplied, it uses the dimensions of counts matrices to set the buffer dimensions.",
      "topics": [
        "defaultBuffer"
      ]
    },
    {
      "page": "InteractionJaggedArray-overlaps",
      "title": "Overlap methods for InteractionJaggedArray",
      "topics": [
        "countOverlaps",
        "countOverlaps,InteractionJaggedArray,InteractionJaggedArray-method",
        "countOverlaps,InteractionJaggedArray,missing-method",
        "countOverlaps,InteractionJaggedArray,Vector-method",
        "findOverlaps",
        "findOverlaps,InteractionJaggedArray,InteractionJaggedArray-method",
        "findOverlaps,InteractionJaggedArray,missing-method",
        "findOverlaps,InteractionJaggedArray,Vector-method",
        "overlapsAny",
        "overlapsAny,InteractionJaggedArray,InteractionJaggedArray-method",
        "overlapsAny,InteractionJaggedArray,missing-method",
        "overlapsAny,InteractionJaggedArray,Vector-method",
        "subsetByOverlaps",
        "subsetByOverlaps,InteractionJaggedArray,InteractionJaggedArray-method",
        "subsetByOverlaps,InteractionJaggedArray,missing-method",
        "subsetByOverlaps,InteractionJaggedArray,Vector-method"
      ]
    },
    {
      "page": "hdf5BlockApply",
      "title": "HDF5-backed blockApply",
      "topics": [
        "hdf5BlockApply",
        "hdf5BlockApply,DelayedArray-method"
      ]
    },
    {
      "page": "InteractionArray-class",
      "title": "InteractionArray Class",
      "topics": [
        "cbind,InteractionArray-method",
        "InteractionArray",
        "InteractionArray,ANY,GInteractions-method",
        "InteractionArray,missing,missing-method",
        "InteractionArray-class",
        "rbind,InteractionArray-method",
        "show,InteractionArray-method"
      ]
    },
    {
      "page": "InteractionJaggedArray-class",
      "title": "InteractionJaggedArray Class",
      "topics": [
        "colData,InteractionJaggedArray-method",
        "counts,InteractionJaggedArray-method",
        "dim,InteractionJaggedArray-method",
        "InteractionJaggedArray",
        "InteractionJaggedArray-class",
        "interactions,InteractionJaggedArray-method",
        "length,InteractionJaggedArray-method",
        "metadata,InteractionJaggedArray-method",
        "path,InteractionJaggedArray-method",
        "show,InteractionJaggedArray-method",
        "[,InteractionJaggedArray,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "InteractionMatrix-class",
      "title": "InteractionMatrix Class",
      "topics": [
        "cbind,InteractionMatrix-method",
        "InteractionMatrix",
        "InteractionMatrix,ANY,GInteractions-method",
        "InteractionMatrix,missing,missing-method",
        "InteractionMatrix-class",
        "rbind,InteractionMatrix-method",
        "show,InteractionMatrix-method"
      ]
    },
    {
      "page": "JaggedArray-class",
      "title": "JaggedArray Class",
      "topics": [
        "as.list,JaggedArray-method",
        "dim,JaggedArray-method",
        "JaggedArray",
        "JaggedArray-class",
        "path,JaggedArray-method",
        "show,JaggedArray-method",
        "[,JaggedArray,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "makeRandomGInteractions",
      "title": "Creating random GRanges & GInteractions",
      "topics": [
        "makeRandomGInteractions",
        "makeRandomGInteractions,Seqinfo-method",
        "makeRandomGRanges",
        "makeRandomGRanges,Seqinfo-method"
      ]
    },
    {
      "page": "MatrixSelection-class",
      "title": "MatrixSelection Class",
      "topics": [
        "MatrixSelection",
        "MatrixSelection-class"
      ]
    },
    {
      "page": "MergedGInteractions-class",
      "title": "MergedGInteractions Class",
      "topics": [
        "MergedGInteractions",
        "MergedGInteractions-class"
      ]
    },
    {
      "page": "mergePairs",
      "title": "Merge sets of paired interactions",
      "topics": [
        "mergePairs",
        "mergePairs,list_OR_SimpleList_OR_GInteractions,numeric-method"
      ]
    },
    {
      "page": "path",
      "title": "Accessor for h5File path from an InteractionMatrix",
      "topics": [
        "path,InteractionMatrix-method",
        "path<-,InteractionMatrix-method"
      ]
    },
    {
      "page": "pileupBoundaries",
      "title": "Pileup Hi-C contacts around boundary regions",
      "topics": [
        "pileupBoundaries",
        "pileupBoundaries,GRanges_OR_GInteractions,character,numeric-method"
      ]
    },
    {
      "page": "pileupDomains",
      "title": "Pileup Hi-C domains",
      "topics": [
        "pileupDomains",
        "pileupDomains,GRanges_OR_GInteractions,character,numeric-method"
      ]
    },
    {
      "page": "pileupPixels",
      "title": "Pileup Hi-C pixels",
      "topics": [
        "pileupPixels",
        "pileupPixels,GInteractions,character,numeric-method"
      ]
    },
    {
      "page": "pixelsToMatrices",
      "title": "Expand pixels to submatrices",
      "topics": [
        "pixelsToMatrices",
        "pixelsToMatrices,GInteractions,numeric-method"
      ]
    },
    {
      "page": "adjustEnrichment",
      "title": "Adjust loop enrichment to remove distance- dependent effect.",
      "topics": [
        "adjustEnrichment",
        "adjustEnrichment,DelayedMatrix_OR_matrix,GInteractions-method",
        "plotEnrichment",
        "plotEnrichment,numeric,GInteractions-method"
      ]
    },
    {
      "page": "plotMatrix",
      "title": "Plot matrix",
      "topics": [
        "plotMatrix",
        "plotMatrix,DelayedMatrix_OR_matrix-method"
      ]
    },
    {
      "page": "pullHicMatrices",
      "title": "Pull submatrices from `.hic` files",
      "topics": [
        "pullHicMatrices",
        "pullHicMatrices,GInteractions,character,numeric-method"
      ]
    },
    {
      "page": "pullHicPixels",
      "title": "Pull contact frequency from `.hic` files",
      "topics": [
        "pullHicPixels",
        "pullHicPixels,GInteractions,character,numeric-method"
      ]
    },
    {
      "page": "regularize",
      "title": "Regularize JaggedArray or InteractionJaggedArray objects",
      "topics": [
        "regularize",
        "regularize,InteractionJaggedArray-method",
        "regularize,JaggedArray-method"
      ]
    },
    {
      "page": "removeShortPairs",
      "title": "Remove interactions that would cross the Hi-C diagonal or a specified distance from the diagonal.",
      "topics": [
        "removeShortPairs",
        "removeShortPairs,GInteractions-method"
      ]
    },
    {
      "page": "selectionMethod",
      "title": "Get selectionMethod from MergedGInteractions object",
      "topics": [
        "selectionMethod",
        "selectionMethod,MergedGInteractions-method"
      ]
    },
    {
      "page": "selectPixel",
      "title": "Get the pixel representing the strongest or weakest interaction in an InteractionArray",
      "topics": [
        "selectPixel",
        "selectPixel,InteractionArray-method"
      ]
    },
    {
      "page": "selection-functions",
      "title": "Visualize selection for a MatrixSelection object",
      "topics": [
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        "selectBlock,numeric-method",
        "selectBottomLeft",
        "selectBottomLeft,numeric-method",
        "selectBottomRight",
        "selectBottomRight,numeric-method",
        "selectCenterPixel",
        "selectCenterPixel,numeric-method",
        "selectCols",
        "selectCols,numeric-method",
        "selectCoordinates",
        "selectCoordinates,numeric-method",
        "selectCorners",
        "selectCorners,numeric-method",
        "selectInner",
        "selectInner,numeric-method",
        "selectOuter",
        "selectOuter,numeric-method",
        "selectRadius",
        "selectRadius,numeric-method",
        "selectRows",
        "selectRows,numeric-method",
        "selectSubmatrix",
        "selectSubmatrix,matrix-method",
        "selectTopLeft",
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        "selectTopRight",
        "selectTopRight,numeric-method",
        "show,MatrixSelection-method"
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    },
    {
      "page": "GInteractions-accessors",
      "title": "Access each portion of a GInteractions-like object",
      "topics": [
        "end1",
        "end1,GInteractions_OR_InteractionSet-method",
        "end2",
        "end2,GInteractions_OR_InteractionSet-method",
        "seqnames1",
        "seqnames1,GInteractions_OR_InteractionSet-method",
        "seqnames2",
        "seqnames2,GInteractions_OR_InteractionSet-method",
        "start1",
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        "start2",
        "start2,GInteractions_OR_InteractionSet-method"
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    },
    {
      "page": "sets",
      "title": "Get each set from a MergedGInteractions object",
      "topics": [
        "sets",
        "sets,MergedGInteractions,character_OR_missing,character_OR_missing-method",
        "sets,MergedGInteractions,character_OR_missing,missing-method",
        "sets,MergedGInteractions,missing,character_OR_missing-method",
        "sets,MergedGInteractions,missing,missing-method"
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    },
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      "page": "shiftRanges",
      "title": "Flexibly shifting GRanges according to strand",
      "topics": [
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        "shiftRanges,GRanges,character_OR_numeric-method"
      ]
    },
    {
      "page": "snapToBins",
      "title": "Snap GRanges or GInteractions to nearest bins",
      "topics": [
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        "snapToBins,GRanges,numeric-method"
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    },
    {
      "page": "sources",
      "title": "Accessor for sources",
      "topics": [
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      "source": "mariner.Rmd",
      "filename": "mariner.html",
      "title": "Introduction to mariner",
      "author": "Eric Davis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Why mariner?",
        "Installation",
        "Key features",
        "Manipulating Paired Ranges",
        "Coercing to and accessing GInteractions",
        "Assigning paired ranges to bins",
        "Clustering & Merging Interactions",
        "Extracting & Aggregating Interactions",
        "Pulling pixels",
        "Pulling submatrices",
        "Aggregating count matrices",
        "Visualizing aggregated matrices",
        "Calculating Loop Enrichment",
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      "created": "2025-08-05 13:04:06",
      "modified": "2025-08-05 13:04:06",
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