{
  "_id": "6a1ac15a1d7bb097a09d829f",
  "Package": "r3Cseq",
  "Version": "1.59.0",
  "Title": "Analysis of Chromosome Conformation Capture and Next-generation\nSequencing (3C-seq)",
  "Author": "Supat Thongjuea, MRC WIMM Centre for Computational Biology,\nWeatherall Institute of Molecular Medicine, University of\nOxford, UK <supat.thongjuea@imm.ox.ac.uk>",
  "Maintainer": "Supat Thongjuea <supat.thongjuea@imm.ox.ac.uk> or\n<supat.thongjuea@gmail.com>",
  "Description": "This package is used for the analysis of long-range\nchromatin interactions from 3C-seq assay.",
  "License": "GPL-3",
  "URL": "http://r3cseq.genereg.net,https://github.com/supatt-lab/r3Cseq/",
  "Collate": "AllClasses.R AllGenerics.R Export.R FunctionInCommon.R\nFunctionsForBatchAnalysis.R RestrictionEnzymeFunctions.R\nFunctionsForNoReplicationAnalysis.R Report.R Visualize3Cseq.R\nAnnotation.R",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:35:59 UTC",
  "RemoteUrl": "https://github.com/bioc/r3Cseq",
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    "getReadCountPerWindow",
    "getViewpoint",
    "plot3Cecdf",
    "plotDomainogramNearViewpoint",
    "plotInteractionsNearViewpoint",
    "plotInteractionsPerChromosome",
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        "calculateBatchRPM,r3CseqInBatch-method"
      ]
    },
    {
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      "title": "calculate read per million (RPM)",
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        "calculateRPM,r3Cseq-method"
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      "page": "contrCoverage",
      "title": "This method has been removed.",
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        "contrCoverage,r3Cseq-method"
      ]
    },
    {
      "page": "contrInteractionRegions",
      "title": "get interaction regions from the control",
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      ]
    },
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        "contrRawData<-",
        "contrRawData<-,r3Cseq-method"
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    },
    {
      "page": "contrReadCount",
      "title": "get read count per region for the control",
      "topics": [
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        "contrReadCount,r3CseqCommon-method"
      ]
    },
    {
      "page": "contrRPM",
      "title": "get read per million (RPM) for the control",
      "topics": [
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        "contrRPM,r3CseqCommon-method"
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    },
    {
      "page": "enzymeDb",
      "title": "Rebase The Restriction Enzyme Database",
      "topics": [
        "enzymeDb"
      ]
    },
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      "page": "expCoverage",
      "title": "This method has been removed.",
      "topics": [
        "expCoverage",
        "expCoverage,r3Cseq-method"
      ]
    },
    {
      "page": "expInteractionRegions",
      "title": "get interaction regions from the experiment",
      "topics": [
        "expInteractionRegions",
        "expInteractionRegions,r3CseqCommon-method"
      ]
    },
    {
      "page": "export3Cseq2bedGraph",
      "title": "export interaction regions to the 'bedGraph' format",
      "topics": [
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        "export3Cseq2bedGraph,r3Cseq-method"
      ]
    },
    {
      "page": "export3CseqRawReads2bedGraph",
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      "topics": [
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        "export3CseqRawReads2bedGraph,r3Cseq-method"
      ]
    },
    {
      "page": "exportBatchInteractions2text",
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      "topics": [
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        "exportBatchInteractions2text,r3CseqInBatch-method"
      ]
    },
    {
      "page": "exportInteractions2text",
      "title": "export identified interaction regions to the tab separated format",
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        "exportInteractions2text,r3Cseq-method"
      ]
    },
    {
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      "title": "Accessors for the 'expRawData' slot of a r3Cseq object.",
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        "expRawData<-",
        "expRawData<-,r3Cseq-method"
      ]
    },
    {
      "page": "expReadCount",
      "title": "get read count per region for the experiment",
      "topics": [
        "expReadCount",
        "expReadCount,r3CseqCommon-method"
      ]
    },
    {
      "page": "expRPM",
      "title": "get read per million (RPM) for the experiment",
      "topics": [
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        "expRPM,r3CseqCommon-method"
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    },
    {
      "page": "generate3CseqReport",
      "title": "generate reports for analysis results from r3Cseq",
      "topics": [
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        "generate3CseqReport,r3Cseq-method",
        "generate3CseqReport,r3CseqInBatch-method"
      ]
    },
    {
      "page": "getBatchInteractions",
      "title": "calculate z-score, assign p-value and q-value for each interaction region for replicates data sets",
      "topics": [
        "getBatchInteractions",
        "getBatchInteractions,r3CseqInBatch-method"
      ]
    },
    {
      "page": "getBatchRawReads",
      "title": "Get aligned reads from the replicates BAM files",
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        "getBatchRawReads,r3CseqInBatch-method"
      ]
    },
    {
      "page": "getBatchReadCountPerRestrictionFragment",
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    {
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        "getBatchReadCountPerWindow,r3CseqInBatch-method"
      ]
    },
    {
      "page": "getContrInteractionsInRefseq",
      "title": "identified significant interaction regions for RefSeq genes",
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        "getContrInteractionsInRefseq,r3Cseq-method"
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        "getExpInteractionsInRefseq,r3Cseq-method"
      ]
    },
    {
      "page": "getInteractions",
      "title": "calculate z-score, assign p-value and q-value for each interaction region",
      "topics": [
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        "getInteractions,r3Cseq-method"
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    {
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        "getRawReads,r3Cseq-method"
      ]
    },
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        "getReadCountPerRestrictionFragment,r3Cseq-method"
      ]
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      "page": "getReadCountPerWindow",
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        "getReadCountPerWindow,r3Cseq-method"
      ]
    },
    {
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        "getViewpoint,r3Cseq-method"
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      "page": "hg18refGene",
      "title": "hg18's refGenes",
      "topics": [
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      "page": "hg19refGene",
      "title": "hg19's refGenes",
      "topics": [
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    {
      "page": "mm10refGene",
      "title": "mm10's refGenes",
      "topics": [
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    {
      "page": "mm9refGene",
      "title": "mm9's refGenes",
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      "page": "plot3Cecdf",
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        "plot3Cecdf",
        "plot3Cecdf,r3Cseq-method"
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    },
    {
      "page": "plotDomainogramNearViewpoint",
      "title": "Plot domainogram of interaction regions near the viewpoint",
      "topics": [
        "plotDomainogramNearViewpoint",
        "plotDomainogramNearViewpoint,r3Cseq-method"
      ]
    },
    {
      "page": "plotInteractionsNearViewpoint",
      "title": "Plot identified interaction regions near the viewpoint",
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        "plotInteractionsNearViewpoint,r3Cseq-method"
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    },
    {
      "page": "plotInteractionsPerChromosome",
      "title": "Plot interaction regions per each chromosome of interest",
      "topics": [
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        "plotInteractionsPerChromosome,r3Cseq-method"
      ]
    },
    {
      "page": "plotOverviewInteractions",
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