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  "Package": "Basic4Cseq",
  "Type": "Package",
  "Title": "Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data",
  "Version": "1.49.0",
  "Date": "2025-06-27",
  "Author": "Carolin Walter",
  "Maintainer": "Carolin Walter <carolin.walter@uni-muenster.de>",
  "Description": "Basic4Cseq is an R/Bioconductor package for basic\nfiltering, analysis and subsequent visualization of 4C-seq\ndata. Virtual fragment libraries can be created for any\nBSGenome package, and filter functions for both reads and\nfragments and basic quality controls are included. Fragment\ndata in the vicinity of the experiment's viewpoint can be\nvisualized as a coverage plot based on a running median\napproach and a multi-scale contact profile.",
  "License": "LGPL-3",
  "biocViews": "ImmunoOncology, Visualization, QualityControl, Sequencing,\nCoverage, Alignment, RNASeq, SequenceMatching, DataImport",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:43 UTC",
  "RemoteUrl": "https://github.com/bioc/Basic4Cseq",
  "RemoteRef": "HEAD",
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    "User": "root"
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  "_type": "src",
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  "_published": "2026-05-31T08:01:13.128Z",
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  "_upstream": "https://github.com/bioc/Basic4Cseq",
  "_commit": {
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    "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",
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  "_maintainer": {
    "name": "Carolin Walter",
    "email": "carolin.walter@uni-muenster.de"
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      "version": ">= 3.5.0",
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      "package": "Biostrings",
      "role": "Depends"
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    {
      "package": "GenomicAlignments",
      "role": "Depends"
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    {
      "package": "caTools",
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    {
      "package": "GenomicRanges",
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    {
      "package": "graphics",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "RCircos",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Ecoli.NCBI.20080805",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Suggests"
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "week": "2025-44",
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  "_bioc": [
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      "branch": "devel",
      "version": "1.49.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.48.0",
      "bioc": "3.23"
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  "_topics": [
    "immunooncology",
    "visualization",
    "qualitycontrol",
    "sequencing",
    "coverage",
    "alignment",
    "rnaseq",
    "sequencematching",
    "dataimport"
  ],
  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
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    "source": "https://www.bioconductor.org/packages/stats/bioc/Basic4Cseq"
  },
  "_searchresults": 11,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "checkRestrictionEnzymeSequence",
    "chooseNearCisFragments",
    "createVirtualFragmentLibrary",
    "Data4Cseq",
    "drawDigestionFragmentHistogram",
    "drawHeatmap",
    "exportVisualizationFragmentData",
    "getReadDistribution",
    "giveEnzymeSequence",
    "importVisualizationFragmentData",
    "nearCisFragments",
    "nearCisFragments<-",
    "normalizeFragmentData",
    "plotTransInteractions",
    "pointsOfInterest",
    "pointsOfInterest<-",
    "prepare4CseqData",
    "printBEDFragmentLibrary",
    "printWigFile",
    "rawFragments",
    "rawFragments<-",
    "rawReads",
    "rawReads<-",
    "readLength",
    "readLength<-",
    "readPointsOfInterestFile",
    "readsToFragments",
    "simulateDigestion",
    "viewpointChromosome",
    "viewpointChromosome<-",
    "viewpointInterval",
    "viewpointInterval<-",
    "visualizeViewpoint"
  ],
  "_datasets": [
    {
      "name": "liverData",
      "title": "Example 4C-seq data set of fetal liver data",
      "object": "liverData",
      "file": "liverData.RData",
      "class": [
        "Data4Cseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "liverDataRaw",
      "title": "Example 4C-seq data set of fetal liver data",
      "object": "liverDataRaw",
      "file": "liverDataRaw.RData",
      "class": [
        "Data4Cseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "checkRestrictionEnzymeSequence",
      "title": "Remove invalid 4C-seq reads from a SAM file",
      "topics": [
        "checkRestrictionEnzymeSequence",
        "checkRestrictionEnzymeSequence,character,character-method"
      ]
    },
    {
      "page": "chooseNearCisFragments",
      "title": "Choose fragments in a provided region around the viewpoint",
      "topics": [
        "chooseNearCisFragments",
        "chooseNearCisFragments,Data4Cseq,numeric-method"
      ]
    },
    {
      "page": "createVirtualFragmentLibrary",
      "title": "Create a virtual fragment library from a provided genome and two restriction enzymes",
      "topics": [
        "createVirtualFragmentLibrary",
        "createVirtualFragmentLibrary,BSgenome,character,character,numeric-method",
        "createVirtualFragmentLibrary,DNAString,character,character,numeric-method"
      ]
    },
    {
      "page": "Data4Cseq",
      "title": "Creating a Data4Cseq object",
      "topics": [
        "Data4Cseq",
        "Data4Cseq,character,numeric,numeric,data.frame,GAlignments-method",
        "Data4Cseq,character,numeric,numeric,missing,missing-method"
      ]
    },
    {
      "page": "Data4Cseq-class",
      "title": "Class '\"Data4Cseq\"'",
      "topics": [
        "Data4Cseq-class",
        "nearCisFragments",
        "nearCisFragments,Data4Cseq-method",
        "nearCisFragments<-",
        "nearCisFragments<-,Data4Cseq,data.frame-method",
        "pointsOfInterest",
        "pointsOfInterest,Data4Cseq-method",
        "pointsOfInterest<-",
        "pointsOfInterest<-,Data4Cseq,data.frame-method",
        "rawFragments",
        "rawFragments,Data4Cseq-method",
        "rawFragments<-",
        "rawFragments<-,Data4Cseq,data.frame-method",
        "rawReads",
        "rawReads,Data4Cseq-method",
        "rawReads<-",
        "rawReads<-,Data4Cseq,GAlignments-method",
        "readLength",
        "readLength,Data4Cseq-method",
        "readLength<-",
        "readLength<-,Data4Cseq,numeric-method",
        "viewpointChromosome",
        "viewpointChromosome,Data4Cseq-method",
        "viewpointChromosome<-",
        "viewpointChromosome<-,Data4Cseq,character-method",
        "viewpointInterval",
        "viewpointInterval,Data4Cseq-method",
        "viewpointInterval<-",
        "viewpointInterval<-,Data4Cseq,numeric-method"
      ]
    },
    {
      "page": "drawDigestionFragmentHistogram",
      "title": "Visualize digestion fragments with a histogram",
      "topics": [
        "drawDigestionFragmentHistogram",
        "drawDigestionFragmentHistogram,data.frame-method"
      ]
    },
    {
      "page": "drawHeatmap",
      "title": "Draw a heatmap-like multi-scale contact profile",
      "topics": [
        "drawHeatmap",
        "drawHeatmap,data.frame-method",
        "drawHeatmap,Data4Cseq-method"
      ]
    },
    {
      "page": "exportVisualizationFragmentData",
      "title": "Export near-cis fragment data of a 'Data4Cseq' object",
      "topics": [
        "exportVisualizationFragmentData",
        "exportVisualizationFragmentData,Data4Cseq,character-method"
      ]
    },
    {
      "page": "getReadDistribution",
      "title": "Calculate the read distribution for a 4C-seq experiment",
      "topics": [
        "getReadDistribution",
        "getReadDistribution,Data4Cseq-method"
      ]
    },
    {
      "page": "giveEnzymeSequence",
      "title": "Provide the corresponding enzyme sequence for an enzyme name",
      "topics": [
        "giveEnzymeSequence",
        "giveEnzymeSequence,character,character-method"
      ]
    },
    {
      "page": "importVisualizationFragmentData",
      "title": "Import visualization data from a file",
      "topics": [
        "importVisualizationFragmentData",
        "importVisualizationFragmentData,character-method"
      ]
    },
    {
      "page": "liverData",
      "title": "Example 4C-seq data set of fetal liver data",
      "topics": [
        "liverData"
      ]
    },
    {
      "page": "liverDataRaw",
      "title": "Example 4C-seq data set of fetal liver data",
      "topics": [
        "liverDataRaw"
      ]
    },
    {
      "page": "normalizeFragmentData",
      "title": "Normalize near-cis fragment data read count",
      "topics": [
        "normalizeFragmentData",
        "normalizeFragmentData,Data4Cseq-method"
      ]
    },
    {
      "page": "plotTransInteractions",
      "title": "Visualize trans interaction intervals",
      "topics": [
        "plotTransInteractions",
        "plotTransInteractions,character,character,numeric,character-method",
        "plotTransInteractions,data.frame,character,numeric,data.frame-method"
      ]
    },
    {
      "page": "prepare4CseqData",
      "title": "Alignment and filtering of raw 4C-seq data",
      "topics": [
        "prepare4CseqData",
        "prepare4CseqData,character,character,character,character-method"
      ]
    },
    {
      "page": "printBEDFragmentLibrary",
      "title": "Print a BED-file fragment library",
      "topics": [
        "printBEDFragmentLibrary",
        "printBEDFragmentLibrary,character,character-method"
      ]
    },
    {
      "page": "printWigFile",
      "title": "Print a wig file from 4C-seq read data",
      "topics": [
        "printWigFile",
        "printWigFile,Data4Cseq-method"
      ]
    },
    {
      "page": "readPointsOfInterestFile",
      "title": "Read a file with coordinates of marker points",
      "topics": [
        "readPointsOfInterestFile",
        "readPointsOfInterestFile,character-method"
      ]
    },
    {
      "page": "readsToFragments",
      "title": "Determine fragment coverage of a 4C-seq fragment library",
      "topics": [
        "readsToFragments",
        "readsToFragments,Data4Cseq,character-method"
      ]
    },
    {
      "page": "simulateDigestion",
      "title": "Simulate the digestion of a genome",
      "topics": [
        "simulateDigestion",
        "simulateDigestion,character,character,BSgenome-method",
        "simulateDigestion,character,character,character-method"
      ]
    },
    {
      "page": "visualizeViewpoint",
      "title": "Draw a near-cis coverage plot for 4C-seq data",
      "topics": [
        "visualizeViewpoint",
        "visualizeViewpoint,data.frame-method",
        "visualizeViewpoint,Data4Cseq-method"
      ]
    }
  ],
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      "filename": "vignette.pdf",
      "title": "Basic4Cseq: an R/Bioconductor package for the analysis of 4C-seq data",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2014-03-20 23:55:49",
      "modified": "2017-08-02 11:09:27",
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