{
  "_id": "6a494af9f6c47c4419498de4",
  "Package": "mariner",
  "Type": "Package",
  "Title": "Mariner: Explore the Hi-Cs",
  "Version": "1.13.0",
  "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.r-universe.dev",
  "Date/Publication": "2026-04-28 13:00:45 UTC",
  "RemoteUrl": "https://github.com/bioc/mariner",
  "RemoteRef": "HEAD",
  "RemoteSha": "9d72228e87c9642e787b2abc1f4dd58b857ffcac",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-03 17:02:51 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>",
  "_user": "bioc",
  "_type": "src",
  "_file": "mariner_1.13.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/df99b5756bca510b9bf3f6ad470024f08df1990a9ae6d2653cb69dd97d83a3d7",
  "_filesize": 974036,
  "_sha256": "df99b5756bca510b9bf3f6ad470024f08df1990a9ae6d2653cb69dd97d83a3d7",
  "_expires": "2026-10-12T18:03:35.000Z",
  "_created": "2026-07-03T17:02:51.000Z",
  "_published": "2026-07-04T18:03:37.228Z",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28673825067",
  "_status": "success",
  "_upstream": "https://github.com/bioc/mariner",
  "_commit": {
    "id": "9d72228e87c9642e787b2abc1f4dd58b857ffcac",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381245
  },
  "_maintainer": {
    "name": "Eric Davis",
    "email": "ericscottdavis@outlook.com",
    "login": "ericsdavis",
    "twitter": "@ericscottdavis1",
    "description": "Bioinformatics Scientist & Software Developer",
    "uuid": 31807001,
    "orcid": "0000-0003-4051-3217"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85154633522,
      "time": 272,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8071807679"
    },
    {
      "job": 85154633526,
      "time": 904,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8071957509"
    },
    {
      "job": 85154633681,
      "time": 1109,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8072004774"
    },
    {
      "job": 85154633542,
      "time": 476,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8071856206"
    },
    {
      "job": 85154633541,
      "time": 532,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8071869426"
    },
    {
      "job": 85154633290,
      "time": 424,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8071743906"
    },
    {
      "job": 85154633575,
      "time": 234,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8071798836"
    },
    {
      "job": 85154633527,
      "time": 1448,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8072081647"
    },
    {
      "job": 85154633689,
      "time": 1628,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8072122677"
    },
    {
      "job": 85154633603,
      "time": 1621,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8072121499"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocManager",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "InteractionSet",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "assertthat",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "dbscan",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "progress",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "strawr",
      "version": ">= 0.0.91",
      "role": "Imports"
    },
    {
      "package": "DelayedArray",
      "role": "Imports"
    },
    {
      "package": "HDF5Array",
      "role": "Imports"
    },
    {
      "package": "abind",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "rhdf5",
      "role": "Imports"
    },
    {
      "package": "plotgardener",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "colourvalues",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "ExperimentHub",
      "role": "Suggests"
    },
    {
      "package": "marinerData",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg38.knownGene",
      "role": "Suggests"
    },
    {
      "package": "fields",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-32",
      "n": 2
    },
    {
      "week": "2025-48",
      "n": 2
    },
    {
      "week": "2026-03",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.13.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.12.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "functionalgenomics",
    "visualization",
    "hic"
  ],
  "_stars": 12,
  "_contributors": [
    {
      "user": "ericsdavis",
      "count": 376,
      "uuid": 31807001
    },
    {
      "user": "sarmapar",
      "count": 16,
      "uuid": 57263711
    },
    {
      "user": "jwokaty",
      "count": 10,
      "uuid": 1744257
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/ericsdavis/mariner",
  "_pkgdown": "https://ericscottdavis.com/mariner/",
  "_searchresults": 252,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/mariner.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "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": [
        "selectBlock",
        "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",
        "selectTopLeft,numeric-method",
        "selectTopRight",
        "selectTopRight,numeric-method",
        "show,MatrixSelection-method"
      ]
    },
    {
      "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",
        "start1,GInteractions_OR_InteractionSet-method",
        "start2",
        "start2,GInteractions_OR_InteractionSet-method"
      ]
    },
    {
      "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"
      ]
    },
    {
      "page": "shiftRanges",
      "title": "Flexibly shifting GRanges according to strand",
      "topics": [
        "shiftRanges",
        "shiftRanges,GRanges,character_OR_numeric-method"
      ]
    },
    {
      "page": "snapToBins",
      "title": "Snap GRanges or GInteractions to nearest bins",
      "topics": [
        "snapToBins",
        "snapToBins,GInteractions,numeric-method",
        "snapToBins,GRanges,numeric-method"
      ]
    },
    {
      "page": "sources",
      "title": "Accessor for sources",
      "topics": [
        "sources",
        "sources,MergedGInteractions-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/mariner/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "assertthat",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cigarillo",
    "cli",
    "codetools",
    "colourvalues",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "dbscan",
    "DelayedArray",
    "digest",
    "dir.expiry",
    "dplyr",
    "farver",
    "filelock",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "ggplotify",
    "glue",
    "gridGraphics",
    "gtable",
    "h5mread",
    "HDF5Array",
    "hms",
    "httr",
    "InteractionSet",
    "IRanges",
    "isoband",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "plotgardener",
    "plyranges",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "strawr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyselect",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "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",
        "Session Info"
      ],
      "created": "2025-08-05 13:04:06",
      "modified": "2025-08-05 13:04:06",
      "commits": 1
    }
  ],
  "_score": 7.35564305022087,
  "_indexed": true,
  "_nocasepkg": "mariner",
  "_universes": [
    "bioc",
    "ericsdavis"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.13.0",
      "date": "2026-07-03T17:08:06.000Z",
      "distro": "resolute",
      "commit": "9d72228e87c9642e787b2abc1f4dd58b857ffcac",
      "fileid": "https://r2.ropensci.org/101c9d69082dc4c6780d5fa2e5cb1064b28423d2b1a135c461c7f41883cb7669",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28673825067"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.13.0",
      "date": "2026-07-03T17:08:06.000Z",
      "distro": "resolute",
      "commit": "9d72228e87c9642e787b2abc1f4dd58b857ffcac",
      "fileid": "https://r2.ropensci.org/fcd23db25e71176f31f88eaa5c429b66413d7867211c50e0fd5e3a42a3978631",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28673825067"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.13.0",
      "date": "2026-07-03T17:05:08.000Z",
      "commit": "9d72228e87c9642e787b2abc1f4dd58b857ffcac",
      "fileid": "https://r2.ropensci.org/47cfb40e7ed3c00b72f891089933a074f5349c58dda5f14b2e551e16306bd293",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28673825067"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.13.0",
      "date": "2026-07-03T17:05:24.000Z",
      "commit": "9d72228e87c9642e787b2abc1f4dd58b857ffcac",
      "fileid": "https://r2.ropensci.org/62dad9669f01f74f1d9bcacf151045b10d489f05648549a02a75ab78e4377d87",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28673825067"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.13.0",
      "date": "2026-07-03T17:07:32.000Z",
      "commit": "9d72228e87c9642e787b2abc1f4dd58b857ffcac",
      "fileid": "https://r2.ropensci.org/ff0ba4d41fc6d843358314a5f3d86888d067932fd04275c6492a97456c227eba",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28673825067"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.13.0",
      "date": "2026-07-03T17:06:04.000Z",
      "commit": "9d72228e87c9642e787b2abc1f4dd58b857ffcac",
      "fileid": "https://r2.ropensci.org/8baaa069dc5da5574c4573ff60b815e69f223e32f677deb7930d7fd48a03c16e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28673825067"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.13.0",
      "date": "2026-07-03T17:06:21.000Z",
      "commit": "9d72228e87c9642e787b2abc1f4dd58b857ffcac",
      "fileid": "https://r2.ropensci.org/6863a82f0f55eb38ea0bd16244dbf7286fa1e8a6839fc67868bc8d1947ccb542",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28673825067"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.13.0",
      "date": "2026-07-03T17:06:31.000Z",
      "commit": "9d72228e87c9642e787b2abc1f4dd58b857ffcac",
      "fileid": "https://r2.ropensci.org/d2b58851ab9e120eb205aca7df01fb6d8b6f56f189fbd0e030bf138d15facce8",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28673825067"
    }
  ]
}