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  "Title": "Scale4C: an R/Bioconductor package for scale-space\ntransformation of 4C-seq data",
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  "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.",
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    "calculateFingerprintMap",
    "calculateScaleSpace",
    "findSingularities",
    "importBasic4CseqData",
    "outputScaleSpaceTree",
    "plotInflectionPoints",
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    "pointsOfInterest",
    "pointsOfInterest<-",
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    "Scale4C",
    "scaleSpace",
    "scaleSpace<-",
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    "singularities<-",
    "viewpoint",
    "viewpoint<-",
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      "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
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  "_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": [
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        "pointsOfInterest,Scale4C-method",
        "pointsOfInterest<-",
        "pointsOfInterest<-,Scale4C,GRanges-method",
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        "rawData,Scale4C-method",
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        "viewpoint",
        "viewpoint,Scale4C-method",
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        "viewpoint<-,Scale4C,numeric-method",
        "viewpointChromosome",
        "viewpointChromosome,Scale4C-method",
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        "Session Information"
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