{
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  "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",
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  "_created": "2026-07-04T22:32:03.000Z",
  "_published": "2026-07-04T22:38:27.045Z",
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    "warning": 1,
    "note": 7
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    "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",
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    "email": "carolin.walter@uni-muenster.de"
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  "_selfowned": true,
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      "n": 2
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    "dataimport",
    "sequencing",
    "coverage"
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    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
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    "extra/NEWS.txt",
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    "manual.pdf"
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  "_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",
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        "viewpointChromosome",
        "viewpointChromosome,Scale4C-method",
        "viewpointChromosome<-",
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      ]
    }
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    "MatrixGenerics",
    "matrixStats",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "smoothie",
    "SparseArray",
    "SummarizedExperiment",
    "XVector"
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  "_nocasepkg": "scale4c",
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