{
  "_id": "6ae774181e2c7b3a4f530593",
  "Package": "Scale4C",
  "Type": "Package",
  "Title": "Scale4C: an R/Bioconductor package for scale-space\ntransformation of 4C-seq data",
  "Version": "1.35.0",
  "Date": "2025-06-27",
  "Author": "Carolin Walter",
  "Maintainer": "Carolin Walter <carolin.walter@uni-muenster.de>",
  "Description": "Scale4C is an R/Bioconductor package for scale-space\ntransformation and visualization of 4C-seq data. The\nscale-space transformation is a multi-scale visualization\ntechnique to transform a 2D signal (e.g. 4C-seq reads on a\ngenomic interval of choice) into a tesselation in the scale\nspace (2D, genomic position x scale factor) by applying\ndifferent smoothing kernels (Gauss, with increasing sigma).\nThis transformation allows for explorative analysis and\ncomparisons of the data's structure with other samples.",
  "License": "LGPL-3",
  "biocViews": "Visualization, QualityControl, DataImport, Sequencing,\nCoverage",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:48 UTC",
  "RemoteUrl": "https://github.com/bioc/Scale4C",
  "RemoteRef": "HEAD",
  "RemoteSha": "c86a0613a478f4c9ad6951ed303d9b34933b70f7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 14:15:39 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "Scale4C_1.35.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/10b18f846b7f018d507e3268df43e3ba439d603fdd87c8b86d0c8e8d9cc65154",
  "_filesize": 5249907,
  "_sha256": "10b18f846b7f018d507e3268df43e3ba439d603fdd87c8b86d0c8e8d9cc65154",
  "_expires": "2027-02-09T17:17:10.000Z",
  "_created": "2026-11-01T14:15:39.000Z",
  "_published": "2026-11-01T17:17:12.678Z",
  "_upstream": "https://github.com/bioc/Scale4C",
  "_status": "success",
  "_maintainer": {
    "name": "Carolin Walter",
    "email": "carolin.walter@uni-muenster.de"
  },
  "_jobs": [
    {
      "job": 124874097100,
      "time": 150,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13087502524"
    },
    {
      "job": 124874097109,
      "time": 294,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13087487874"
    },
    {
      "job": 124874097078,
      "time": 293,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13087338040"
    },
    {
      "job": 124874097101,
      "time": 183,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13092704670"
    },
    {
      "job": 124874097086,
      "time": 220,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13093001634"
    },
    {
      "job": 124867537358,
      "time": 226,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13086693381"
    },
    {
      "job": 124874097091,
      "time": 86,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13088075343"
    },
    {
      "job": 124874097120,
      "time": 170,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13087795092"
    },
    {
      "job": 124874097097,
      "time": 135,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13087102340"
    },
    {
      "job": 124874097130,
      "time": 165,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13087500639"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41310653711",
  "_commit": {
    "id": "c86a0613a478f4c9ad6951ed303d9b34933b70f7",
    "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": 1777380348
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "smoothie",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "IRanges",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.35.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.34.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "visualization",
    "qualitycontrol",
    "dataimport",
    "sequencing",
    "coverage"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 600,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Scale4C"
  },
  "_searchresults": 3,
  "_abi": {
    "exports": [
      {
        "key": "Scale4C::Scale4C",
        "hash": "e370c235a6f50811"
      },
      {
        "key": "Scale4C::generic:Scale4C",
        "hash": "13a8fb352416379c"
      },
      {
        "key": "Scale4C::generic:addPointsOfInterest",
        "hash": "cf077b9d357ef96c"
      },
      {
        "key": "Scale4C::generic:calculateFingerprintMap",
        "hash": "4637689f121e05c4"
      },
      {
        "key": "Scale4C::generic:calculateScaleSpace",
        "hash": "ea2073218100bf84"
      },
      {
        "key": "Scale4C::generic:findSingularities",
        "hash": "8dfcd167278f1d80"
      },
      {
        "key": "Scale4C::generic:importBasic4CseqData",
        "hash": "c69fdad6275751a4"
      },
      {
        "key": "Scale4C::generic:outputScaleSpaceTree",
        "hash": "4f1a4f401f92eec5"
      },
      {
        "key": "Scale4C::generic:plotInflectionPoints",
        "hash": "18e211b0287ce761"
      },
      {
        "key": "Scale4C::generic:plotTesselation",
        "hash": "6c56d33c16cf7147"
      },
      {
        "key": "Scale4C::generic:plotTraceback",
        "hash": "f128bdb25b86d0f0"
      },
      {
        "key": "Scale4C::generic:pointsOfInterest",
        "hash": "6c03475c1324e304"
      },
      {
        "key": "Scale4C::generic:pointsOfInterest<-",
        "hash": "46c83034ba2b5242"
      },
      {
        "key": "Scale4C::generic:rawData",
        "hash": "72faad91227f2e7d"
      },
      {
        "key": "Scale4C::generic:rawData<-",
        "hash": "115484f4229928c5"
      },
      {
        "key": "Scale4C::generic:scaleSpace",
        "hash": "24029510ae8b88a1"
      },
      {
        "key": "Scale4C::generic:scaleSpace<-",
        "hash": "01dbb5284f72cfaa"
      },
      {
        "key": "Scale4C::generic:singularities",
        "hash": "1d0c9b8349872ebe"
      },
      {
        "key": "Scale4C::generic:singularities<-",
        "hash": "623a523b4c28ab08"
      },
      {
        "key": "Scale4C::generic:traceContour",
        "hash": "6e52ca0d60268e72"
      },
      {
        "key": "Scale4C::generic:viewpoint",
        "hash": "9599aeae79126167"
      },
      {
        "key": "Scale4C::generic:viewpoint<-",
        "hash": "2c5055d2fc49296e"
      },
      {
        "key": "Scale4C::generic:viewpointChromosome",
        "hash": "481b891a1280b12b"
      },
      {
        "key": "Scale4C::generic:viewpointChromosome<-",
        "hash": "120c4cc01c798722"
      }
    ],
    "imports": []
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/Scale4C.html"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addPointsOfInterest",
    "calculateFingerprintMap",
    "calculateScaleSpace",
    "findSingularities",
    "importBasic4CseqData",
    "outputScaleSpaceTree",
    "plotInflectionPoints",
    "plotTesselation",
    "plotTraceback",
    "pointsOfInterest",
    "pointsOfInterest<-",
    "rawData",
    "rawData<-",
    "Scale4C",
    "scaleSpace",
    "scaleSpace<-",
    "singularities",
    "singularities<-",
    "viewpoint",
    "viewpoint<-",
    "viewpointChromosome",
    "viewpointChromosome<-"
  ],
  "_datasets": [
    {
      "name": "liverData",
      "title": "Example 4C-seq data set of fetal liver data",
      "object": "liverData",
      "file": "liverData.RData",
      "class": [
        "Scale4C"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "liverDataVP",
      "title": "Example 4C-seq data set of fetal liver data, with added VP",
      "object": "liverDataVP",
      "file": "liverDataVP.RData",
      "class": [
        "Scale4C"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "addPointsOfInterest",
      "title": "Add points of interest to a 'Scale4C' object",
      "topics": [
        "addPointsOfInterest",
        "addPointsOfInterest,Scale4C,data.frame-method"
      ]
    },
    {
      "page": "calculateFingerprintMap",
      "title": "Calculate scale-space fingerprint map for given 4C-seq data",
      "topics": [
        "calculateFingerprintMap",
        "calculateFingerprintMap,Scale4C-method"
      ]
    },
    {
      "page": "calculateScaleSpace",
      "title": "Calculate scale-space representation for given 4C-seq data",
      "topics": [
        "calculateScaleSpace",
        "calculateScaleSpace,Scale4C-method"
      ]
    },
    {
      "page": "findSingularities",
      "title": "Find singularities in a provided scale-space fingerprint map",
      "topics": [
        "findSingularities",
        "findSingularities,Scale4C-method"
      ]
    },
    {
      "page": "importBasic4CseqData",
      "title": "Import raw data from a provided Basic4Cseq output file",
      "topics": [
        "importBasic4CseqData",
        "importBasic4CseqData,character,numeric,character,numeric-method"
      ]
    },
    {
      "page": "liverData",
      "title": "Example 4C-seq data set of fetal liver data",
      "topics": [
        "liverData"
      ]
    },
    {
      "page": "liverDataVP",
      "title": "Example 4C-seq data set of fetal liver data, with added VP",
      "topics": [
        "liverDataVP"
      ]
    },
    {
      "page": "outputScaleSpaceTree",
      "title": "Output list of all features for a given scale-space map",
      "topics": [
        "outputScaleSpaceTree",
        "outputScaleSpaceTree,Scale4C-method"
      ]
    },
    {
      "page": "plotInflectionPoints",
      "title": "Draw a smoothed near-cis profile with marked inflection points for a 4C-seq signal",
      "topics": [
        "plotInflectionPoints",
        "plotInflectionPoints,Scale4C,numeric-method"
      ]
    },
    {
      "page": "plotTesselation",
      "title": "Draw the final scale space tesselation",
      "topics": [
        "plotTesselation",
        "plotTesselation,Scale4C-method"
      ]
    },
    {
      "page": "plotTraceback",
      "title": "Draw the traceback results for a list of singular points on a fingerprint map",
      "topics": [
        "plotTraceback",
        "plotTraceback,Scale4C-method"
      ]
    },
    {
      "page": "Scale4C",
      "title": "Creating a Scale4C object",
      "topics": [
        "Scale4C",
        "Scale4C,numeric,character,GRanges-method"
      ]
    },
    {
      "page": "Scale4C-class",
      "title": "Class '\"Scale4C\"'",
      "topics": [
        "pointsOfInterest",
        "pointsOfInterest,Scale4C-method",
        "pointsOfInterest<-",
        "pointsOfInterest<-,Scale4C,GRanges-method",
        "rawData",
        "rawData,Scale4C-method",
        "rawData<-",
        "rawData<-,Scale4C,GRanges-method",
        "Scale4C-class",
        "scaleSpace",
        "scaleSpace,Scale4C-method",
        "scaleSpace<-",
        "scaleSpace<-,Scale4C,SummarizedExperiment-method",
        "singularities",
        "singularities,Scale4C-method",
        "singularities<-",
        "singularities<-,Scale4C,GRanges-method",
        "viewpoint",
        "viewpoint,Scale4C-method",
        "viewpoint<-",
        "viewpoint<-,Scale4C,numeric-method",
        "viewpointChromosome",
        "viewpointChromosome,Scale4C-method",
        "viewpointChromosome<-",
        "viewpointChromosome<-,Scale4C,character-method"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "DelayedArray",
    "generics",
    "GenomicRanges",
    "IRanges",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "smoothie",
    "SparseArray",
    "SummarizedExperiment",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "vignette.Rnw",
      "filename": "vignette.pdf",
      "title": "Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Scale-space transformation of 4C-seq data",
        "Session Information"
      ],
      "created": "2017-06-22 19:42:39",
      "modified": "2017-06-22 19:42:39",
      "commits": 1
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "scale4c",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-11-01T14:37:00.000Z",
      "distro": "resolute",
      "commit": "c86a0613a478f4c9ad6951ed303d9b34933b70f7",
      "fileid": "https://r2.ropensci.org/b28bf7f73dd4202c2023dde997e8813476f61cb057dfd0304c26b7bd88668ea5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310653711"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-11-01T14:37:15.000Z",
      "distro": "resolute",
      "commit": "c86a0613a478f4c9ad6951ed303d9b34933b70f7",
      "fileid": "https://r2.ropensci.org/7ac725c687a7b7bc444c70ec817666958361e7f11ebdff4d1c9036de9bf36776",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310653711"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-11-01T17:15:02.000Z",
      "commit": "c86a0613a478f4c9ad6951ed303d9b34933b70f7",
      "fileid": "https://r2.ropensci.org/4a8a6765e869122951fa239be17f9accb0a38285d34148b122d1ac193ee4f336",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310653711"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-11-01T17:14:53.000Z",
      "commit": "c86a0613a478f4c9ad6951ed303d9b34933b70f7",
      "fileid": "https://r2.ropensci.org/7048629f622e1330f4076f4c09d3ec8ac9cada6a868b987384de33167cb2f627",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310653711"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.35.0",
      "date": "2026-11-01T14:35:36.000Z",
      "commit": "c86a0613a478f4c9ad6951ed303d9b34933b70f7",
      "fileid": "https://r2.ropensci.org/eae211eb9f56f4a3855670148c9b52456996d3d562bfd68b64cc3c0d0e6bfa28",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310653711"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-11-01T14:18:22.000Z",
      "commit": "c86a0613a478f4c9ad6951ed303d9b34933b70f7",
      "fileid": "https://r2.ropensci.org/dcd28cc6fa7c987bfd142854cd7aa7838c1050dc7ddfc172e82504484306733a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310653711"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-11-01T14:18:20.000Z",
      "commit": "c86a0613a478f4c9ad6951ed303d9b34933b70f7",
      "fileid": "https://r2.ropensci.org/d7bdf512a70b687be7ea7dc3725d6b3d0e3eaaef989e92bbc54319b026cfe304",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310653711"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-11-01T14:18:19.000Z",
      "commit": "c86a0613a478f4c9ad6951ed303d9b34933b70f7",
      "fileid": "https://r2.ropensci.org/0159ccc145c4baa3e67b03168eeca1fff8c464f6943858eca00f0755455e7ea1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310653711"
    }
  ]
}