{
  "_id": "6a1fe157b401979e73439d11",
  "Package": "heatmaps",
  "Title": "Flexible Heatmaps for Functional Genomics and Sequence Features",
  "Version": "1.37.0",
  "Date": "2025-07-22",
  "Author": "Malcolm Perry <mgperry32@gmail.com>",
  "Maintainer": "Malcolm Perry <mgperry32@gmail.com>",
  "biocViews": "Visualization, SequenceMatching, FunctionalGenomics",
  "License": "Artistic-2.0",
  "Description": "This package provides functions for plotting heatmaps of\ngenome-wide data across genomic intervals, such as ChIP-seq\nsignals at peaks or across promoters. Many functions are also\nprovided for investigating sequence features.",
  "VignetteBuilder": "knitr",
  "Collate": "Heatmap-class.R PlotHeatmap.R PlotHeatmapList.R\nPlotPatternDensityMap.R PWMScanHeatmap.R PatternHeatmap.R\nCoverageHeatmap.R SmoothHeatmap.R PlotHeatmapMeta.R Data.R",
  "NeedsCompilation": "no",
  "RoxygenNote": "6.0.1",
  "Config/pak/sysreqs": "cmake libfftw3-dev make libjpeg-dev libpng-dev\nlibtiff-dev libuv1-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:38 UTC",
  "RemoteUrl": "https://github.com/bioc/heatmaps",
  "RemoteRef": "HEAD",
  "RemoteSha": "1aa6a5611b6ff0888b3c185c108474c88cc9a0ea",
  "Packaged": {
    "Date": "2026-06-03 07:58:04 UTC",
    "User": "root"
  },
  "MD5sum": "6c8fbbaad1b995eec60306017025e3c5",
  "_user": "bioc",
  "_type": "src",
  "_file": "heatmaps_1.37.0.tar.gz",
  "_fileid": "78e13bd48c6e3b25d9400cae34c3aac300c822eb27a145e59e854ca0c1961994",
  "_filesize": 6955224,
  "_sha256": "78e13bd48c6e3b25d9400cae34c3aac300c822eb27a145e59e854ca0c1961994",
  "_created": "2026-06-03T07:58:04.000Z",
  "_published": "2026-06-03T08:09:59.702Z",
  "_jobs": [
    {
      "job": 79248083877,
      "time": 208,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7378918969"
    },
    {
      "job": 79248083953,
      "time": 317,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7378956380"
    },
    {
      "job": 79248083898,
      "time": 303,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7378951101"
    },
    {
      "job": 79248083876,
      "time": 140,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7378895350"
    },
    {
      "job": 79248083892,
      "time": 234,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7378927631"
    },
    {
      "job": 79247215369,
      "time": 324,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7378846392"
    },
    {
      "job": 79248083871,
      "time": 191,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378912769"
    },
    {
      "job": 79248083923,
      "time": 662,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7379072370"
    },
    {
      "job": 79248083890,
      "time": 554,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7379036340"
    },
    {
      "job": 79248083894,
      "time": 626,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7379059770"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 10
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26871339165",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/heatmaps",
  "_commit": {
    "id": "1aa6a5611b6ff0888b3c185c108474c88cc9a0ea",
    "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": 1777380338
  },
  "_maintainer": {
    "name": "Malcolm Perry",
    "email": "mgperry32@gmail.com",
    "login": "mgperry",
    "description": "Computational Biologist",
    "uuid": 4436672
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "KernSmooth",
      "role": "Imports"
    },
    {
      "package": "plotrix",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "EBImage",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Drerio.UCSC.danRer7",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.37.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.36.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "visualization",
    "sequencematching",
    "functionalgenomics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 700,
    "source": "https://www.bioconductor.org/packages/stats/bioc/heatmaps"
  },
  "_mentions": 3,
  "_searchresults": 19,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/heatmaps.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "coords",
    "coords<-",
    "CoverageHeatmap",
    "default_color",
    "getScale",
    "Heatmap",
    "heatmapOptions",
    "image",
    "image<-",
    "label",
    "label<-",
    "metadata",
    "metadata<-",
    "nseq",
    "nseq<-",
    "PatternHeatmap",
    "plot_clusters",
    "plot_legend",
    "plotHeatmap",
    "plotHeatmapList",
    "plotHeatmapMeta",
    "plotPatternDensityMap",
    "PWMScanHeatmap",
    "rev",
    "scale",
    "scale<-",
    "smoothHeatmap",
    "width",
    "xm",
    "ym"
  ],
  "_datasets": [
    {
      "name": "hm",
      "title": "Data for man page examples",
      "object": "HeatmapExamples",
      "file": "HeatmapExamples.RData",
      "class": [
        "Heatmap"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hm2",
      "title": "Data for man page examples",
      "object": "HeatmapExamples",
      "file": "HeatmapExamples.RData",
      "class": [
        "Heatmap"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mat",
      "title": "Data for man page examples",
      "object": "HeatmapExamples",
      "file": "HeatmapExamples.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "1",
        "2",
        "3",
        "4",
        "5",
        "6",
        "7",
        "8",
        "9",
        "10",
        "11",
        "12",
        "13",
        "14",
        "15",
        "16",
        "17",
        "18",
        "19",
        "20",
        "21",
        "22",
        "23",
        "24",
        "25",
        "26",
        "27",
        "28",
        "29",
        "30",
        "31",
        "32",
        "33",
        "34",
        "35",
        "36",
        "37",
        "38",
        "39",
        "40",
        "41",
        "42",
        "43",
        "44",
        "45",
        "46",
        "47",
        "48",
        "49",
        "50",
        "51",
        "52",
        "53",
        "54",
        "55",
        "56",
        "57",
        "58",
        "59",
        "60",
        "61",
        "62",
        "63",
        "64",
        "65",
        "66",
        "67",
        "68",
        "69",
        "70",
        "71",
        "72",
        "73",
        "74",
        "75",
        "76",
        "77",
        "78",
        "79",
        "80",
        "81",
        "82",
        "83",
        "84",
        "85",
        "86",
        "87",
        "88",
        "89",
        "90",
        "91",
        "92",
        "93",
        "94",
        "95",
        "96",
        "97",
        "98",
        "99",
        "100",
        "101",
        "102",
        "103",
        "104",
        "105",
        "106",
        "107",
        "108",
        "109",
        "110",
        "111",
        "112",
        "113",
        "114",
        "115",
        "116",
        "117",
        "118",
        "119",
        "120",
        "121",
        "122",
        "123",
        "124",
        "125",
        "126",
        "127",
        "128",
        "129",
        "130",
        "131",
        "132",
        "133",
        "134",
        "135",
        "136",
        "137",
        "138",
        "139",
        "140",
        "141",
        "142",
        "143",
        "144",
        "145",
        "146",
        "147",
        "148",
        "149",
        "150",
        "151",
        "152",
        "153",
        "154",
        "155",
        "156",
        "157",
        "158",
        "159",
        "160",
        "161",
        "162",
        "163",
        "164",
        "165",
        "166",
        "167",
        "168",
        "169",
        "170",
        "171",
        "172",
        "173",
        "174",
        "175",
        "176",
        "177",
        "178",
        "179",
        "180",
        "181",
        "182",
        "183",
        "184",
        "185",
        "186",
        "187",
        "188",
        "189",
        "190",
        "191",
        "192",
        "193",
        "194",
        "195",
        "196",
        "197",
        "198",
        "199",
        "200"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "rle_list",
      "title": "Data for man page examples",
      "object": "HeatmapExamples",
      "file": "HeatmapExamples.RData",
      "class": [
        "CompressedRleList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "string_set",
      "title": "Data for man page examples",
      "object": "HeatmapExamples",
      "file": "HeatmapExamples.RData",
      "class": [
        "DNAStringSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "tata_pwm",
      "title": "Data for man page examples",
      "object": "HeatmapExamples",
      "file": "HeatmapExamples.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "windows",
      "title": "Data for man page examples",
      "object": "HeatmapExamples",
      "file": "HeatmapExamples.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "coords",
      "title": "Return or set the coords in a Heatmap",
      "topics": [
        "coords",
        "coords,Heatmap-method",
        "coords<-",
        "coords<-,Heatmap-method"
      ]
    },
    {
      "page": "CoverageHeatmap",
      "title": "Generate a Heatmap of coverage",
      "topics": [
        "CoverageHeatmap",
        "CoverageHeatmap,GenomicRanges,GenomicRanges-method",
        "CoverageHeatmap,GenomicRanges,RleList-method"
      ]
    },
    {
      "page": "default_color",
      "title": "Predifined color palettes from RColorBrewer + Rainbow",
      "topics": [
        "default_color"
      ]
    },
    {
      "page": "getScale",
      "title": "Make an appropriate scale for a heatmap",
      "topics": [
        "getScale"
      ]
    },
    {
      "page": "Heatmap",
      "title": "Function to create a heatmap object",
      "topics": [
        "Heatmap"
      ]
    },
    {
      "page": "Heatmap-class",
      "title": "An S4 class to represent a heatmap",
      "topics": [
        "Heatmap-class"
      ]
    },
    {
      "page": "HeatmapExamples",
      "title": "Data for man page examples",
      "topics": [
        "HeatmapExamples",
        "hm",
        "hm2",
        "mat",
        "rle_list",
        "string_set",
        "tata_pwm",
        "windows"
      ]
    },
    {
      "page": "heatmapOptions",
      "title": "Generate default options for a Heatmap",
      "topics": [
        "heatmapOptions"
      ]
    },
    {
      "page": "image",
      "title": "Return or set the image in a Heatmap",
      "topics": [
        "image",
        "image,Heatmap-method",
        "image<-",
        "image<-,Heatmap-method"
      ]
    },
    {
      "page": "label",
      "title": "Return or set the label in a Heatmap",
      "topics": [
        "label",
        "label,Heatmap-method",
        "label<-",
        "label<-,Heatmap-method"
      ]
    },
    {
      "page": "length-Heatmap-method",
      "title": "Return the number of sequences in a heatmap",
      "topics": [
        "length,Heatmap-method"
      ]
    },
    {
      "page": "metadata",
      "title": "Return or set the metadata in a Heatmap",
      "topics": [
        "metadata",
        "metadata,Heatmap-method",
        "metadata<-",
        "metadata<-,Heatmap-method"
      ]
    },
    {
      "page": "nseq",
      "title": "Return or set nseq in a Heatmap",
      "topics": [
        "nseq",
        "nseq,Heatmap-method",
        "nseq<-",
        "nseq<-,Heatmap-method"
      ]
    },
    {
      "page": "PatternHeatmap",
      "title": "Generate a Heatmap of patterns in DNA sequence",
      "topics": [
        "PatternHeatmap",
        "PatternHeatmap,DNAStringSet,character-method",
        "PatternHeatmap,DNAStringSet,matrix-method"
      ]
    },
    {
      "page": "plot_clusters",
      "title": "Plot partition in a separate panel",
      "topics": [
        "plot_clusters"
      ]
    },
    {
      "page": "plot_legend",
      "title": "Plot a color legend for a heatmap",
      "topics": [
        "plot_legend"
      ]
    },
    {
      "page": "plotHeatmap",
      "title": "Plot a Heatmap object to the device",
      "topics": [
        "plotHeatmap",
        "plotHeatmap,Heatmap-method"
      ]
    },
    {
      "page": "plotHeatmapList",
      "title": "Plot a list of heatmaps",
      "topics": [
        "plotHeatmapList"
      ]
    },
    {
      "page": "plotHeatmapMeta",
      "title": "Plot a Meta-region plot from heatmaps",
      "topics": [
        "plotHeatmapMeta"
      ]
    },
    {
      "page": "plotPatternDensityMap",
      "title": "Plot heatmaps for several patterns in DNA sequence",
      "topics": [
        "plotPatternDensityMap",
        "plotPatternDensityMap,DNAStringSet-method"
      ]
    },
    {
      "page": "PWMScanHeatmap",
      "title": "Generate a Heatmap of PWM Scores in DNA sequnce",
      "topics": [
        "PWMScanHeatmap",
        "PWMScanHeatmap,DNAStringSet,matrix-method"
      ]
    },
    {
      "page": "rev-Heatmap-method",
      "title": "Reflect a heatmap in the x axis",
      "topics": [
        "rev,Heatmap-method"
      ]
    },
    {
      "page": "scale",
      "title": "Return or set the scale in a Heatmap",
      "topics": [
        "scale",
        "scale,Heatmap-method",
        "scale<-",
        "scale<-,Heatmap-method"
      ]
    },
    {
      "page": "smoothHeatmap",
      "title": "Smooth a heatmap",
      "topics": [
        "smoothHeatmap",
        "smoothHeatmap,Heatmap-method"
      ]
    },
    {
      "page": "width-Heatmap-method",
      "title": "Return the width of sequence represented in a heatmap",
      "topics": [
        "width,Heatmap-method"
      ]
    },
    {
      "page": "xm",
      "title": "Generate co-ordinates for each row of the image matrix of a Heatmap",
      "topics": [
        "xm",
        "xm,Heatmap-method"
      ]
    },
    {
      "page": "ym",
      "title": "Generate co-ordinates for each column of the image matrix of a Heatmap",
      "topics": [
        "ym",
        "ym,Heatmap-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/heatmaps/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "base64enc",
    "BiocGenerics",
    "Biostrings",
    "bitops",
    "bslib",
    "cachem",
    "cli",
    "crayon",
    "digest",
    "EBImage",
    "evaluate",
    "fastmap",
    "fftwtools",
    "fontawesome",
    "fs",
    "generics",
    "GenomicRanges",
    "highr",
    "htmltools",
    "htmlwidgets",
    "IRanges",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "lattice",
    "lifecycle",
    "locfit",
    "Matrix",
    "memoise",
    "mime",
    "plotrix",
    "png",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "RCurl",
    "rlang",
    "rmarkdown",
    "S4Vectors",
    "sass",
    "Seqinfo",
    "tiff",
    "tinytex",
    "xfun",
    "XVector",
    "yaml"
  ],
  "_score": 3.931966114728173,
  "_indexed": true,
  "_nocasepkg": "heatmaps",
  "_universes": [
    "bioc",
    "mgperry"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-06-03T08:02:20.000Z",
      "distro": "noble",
      "commit": "1aa6a5611b6ff0888b3c185c108474c88cc9a0ea",
      "fileid": "c8a8ba7e6cbb58474c61b6116a26ea7a679ecd7f124576d12bd1ed5821aa5a3e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871339165"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-06-03T08:02:07.000Z",
      "distro": "noble",
      "commit": "1aa6a5611b6ff0888b3c185c108474c88cc9a0ea",
      "fileid": "5d66ffdb40847d0c8dd4d7d876540292c7071e4b8b8995851862e4eb84616337",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871339165"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-06-03T08:00:02.000Z",
      "commit": "1aa6a5611b6ff0888b3c185c108474c88cc9a0ea",
      "fileid": "8cf11a791583c864a8b5346b959646b9621a171ad52471c7c9cac39cf73d0cf6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871339165"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-06-03T08:01:04.000Z",
      "commit": "1aa6a5611b6ff0888b3c185c108474c88cc9a0ea",
      "fileid": "8bd6226354be8b9186b27de4efc291308fc0657fa3375b0e039556d6dd720453",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871339165"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.37.0",
      "date": "2026-06-03T08:01:39.000Z",
      "commit": "1aa6a5611b6ff0888b3c185c108474c88cc9a0ea",
      "fileid": "e07f6999045787b58a8fddcaca36e2e8c6617f3af1b0b430068fbf52fad85c95",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871339165"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-06-03T08:08:01.000Z",
      "commit": "1aa6a5611b6ff0888b3c185c108474c88cc9a0ea",
      "fileid": "7fa34eadb0623b2537f3e8f5d23d50fa47daea1282f7d229dc4e0a20f7d91db7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871339165"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-06-03T08:06:29.000Z",
      "commit": "1aa6a5611b6ff0888b3c185c108474c88cc9a0ea",
      "fileid": "36d9439c62047271be8281ab3ececdaf9df3d240814d1ce883018a7d1d313f0f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871339165"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-06-03T08:07:25.000Z",
      "commit": "1aa6a5611b6ff0888b3c185c108474c88cc9a0ea",
      "fileid": "07c5128336359795d986b80b6c98cc1172b0c64770346417baa8b646b084d02e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871339165"
    }
  ]
}