{
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  "Package": "DMRcaller",
  "Type": "Package",
  "Title": "Differentially Methylated Regions Caller",
  "Version": "1.45.0",
  "Date": "2019-01-18",
  "Encoding": "UTF-8",
  "Authors@R": "c(person(given=\"Nicolae Radu\", family=\"Zabet\", role =\nc(\"aut\",\"cre\"), email = \"r.zabet@qmul.ac.uk\"),\nperson(given=\"Jonathan\", family=\"Tsang\", role = \"aut\", email =\n\"jmft2@cam.ac.uk\"), person(given=\"Alessandro\", family=\"Greco\",\nrole = \"aut\", email = \"apgrec@essex.ac.uk\"), person(given=\"Ryan\",\nfamily=\"Merritt\", role = \"aut\", email = \"rmerri@essex.ac.uk\"), person(given=\"Young Jun\",\nfamily=\"Kim\", role = \"aut\", email = \"qc25039@qmul.ac.uk\"))",
  "Author": "Nicolae Radu Zabet <r.zabet@qmul.ac.uk>, Jonathan Michael\nFoonlan Tsang <jmft2@cam.ac.uk>, Alessandro Pio Greco\n<apgrec@essex.ac.uk>, Ryan Merritt <rmerri@essex.ac.uk> and\nYoung Jun Kim <qc25039@qmul.ac.uk>",
  "Maintainer": "Nicolae Radu Zabet <r.zabet@qmul.ac.uk>",
  "Description": "Uses Bisulfite sequencing data in two conditions and\nidentifies differentially methylated regions between the\nconditions in CG and non-CG context. The input is the CX report\nfiles produced by Bismark and the output is a list of DMRs\nstored as GRanges objects.",
  "License": "GPL-3",
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  "biocViews": "DifferentialMethylation, DNAMethylation, Software,\nSequencing, Coverage",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:41:01 UTC",
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    "coverage"
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  "_exports": [
    "analyseReadsInsideRegionsForCondition",
    "analyseReadsInsideRegionsForConditionPMD",
    "computeCoMethylatedPositions",
    "computeCoMethylatedRegions",
    "computeDMRs",
    "computeDMRsReplicates",
    "computeMethylationDataCoverage",
    "computeMethylationDataSpatialCorrelation",
    "computeMethylationProfile",
    "computeOverlapProfile",
    "computePMDs",
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    "filterVMDs",
    "filterVMRsONT",
    "getWholeChromosomes",
    "joinReplicates",
    "mergeDMRsIteratively",
    "mergePMDsIteratively",
    "plotLocalMethylationProfile",
    "plotMethylationDataCoverage",
    "plotMethylationDataSpatialCorrelation",
    "plotMethylationProfile",
    "plotMethylationProfileFromData",
    "plotOverlapProfile",
    "poolMethylationDatasets",
    "poolTwoMethylationDatasets",
    "readBismark",
    "readBismarkPool",
    "readONTbam",
    "saveBismark",
    "selectCytosine"
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      "title": "The DMRs between WT and met1-3 in CG context",
      "object": "DMRsNoiseFilterCG",
      "file": "DMRsNoiseFilterCG.RData",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "GEs",
      "title": "The genetic elements data",
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      "file": "GEs.RData",
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      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "GEs_hg38",
      "title": "The genetic elements data of GRCh38 Genome Reference",
      "object": "GEs_hg38",
      "file": "GEs_hg38.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "methylationDataList",
      "title": "The methylation data list",
      "object": "methylationDataList",
      "file": "methylationDataList.RData",
      "class": [
        "CompressedGRangesList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ont_gr_GM18870_chr1_PMD_bins_1k",
      "title": "Partially Methilated Domains example",
      "object": "ont_gr_GM18870_chr1_PMD_bins_1k",
      "file": "ont_gr_GM18870_chr1_PMD_bins_1k.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ont_gr_GM18870_chr1_sorted_bins_1k",
      "title": "The ONT methylation data example",
      "object": "ont_gr_GM18870_chr1_sorted_bins_1k",
      "file": "ont_gr_GM18870_chr1_sorted_bins_1k.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ontSampleGRangesList",
      "title": "The ONT methylation data list",
      "object": "ontSampleGRangesList",
      "file": "ontSampleGRangesList.RData",
      "class": [
        "CompressedGRangesList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "PMDsBinsCG",
      "title": "The PMDs between GM18501 and GM18876 using Bins method",
      "object": "PMDsBinsCG",
      "file": "PMDsBinsCG.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "PMDsNoiseFilterCG",
      "title": "The PMDs between GM18501 and GM18876 using Noise_filter method",
      "object": "PMDsNoiseFilterCG",
      "file": "PMDsNoiseFilterCG.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "syntheticDataReplicates",
      "title": "Simulated data for biological replicates",
      "object": "syntheticDataReplicates",
      "file": "syntheticDataReplicates.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "analyseReadsInsideRegionsForCondition",
      "title": "Analyse reads inside regions for condition",
      "topics": [
        "analyseReadsInsideRegionsForCondition"
      ]
    },
    {
      "page": "analyseReadsInsideRegionsForConditionPMD",
      "title": "Analyse reads inside regions for condition",
      "topics": [
        "analyseReadsInsideRegionsForConditionPMD"
      ]
    },
    {
      "page": "computeCoMethylatedPositions",
      "title": "Compute pairwise co-methylation statistics for cytosine sites within regions",
      "topics": [
        "computeCoMethylatedPositions"
      ]
    },
    {
      "page": "computeCoMethylatedRegions",
      "title": "Compute pairwise co-methylation statistics between regions",
      "topics": [
        "computeCoMethylatedRegions"
      ]
    },
    {
      "page": "computeDMRs",
      "title": "Compute DMRs",
      "topics": [
        "computeDMRs"
      ]
    },
    {
      "page": "computeDMRsReplicates",
      "title": "Compute DMRs",
      "topics": [
        "computeDMRsReplicates"
      ]
    },
    {
      "page": "computeMethylationDataCoverage",
      "title": "Compute methylation data coverage",
      "topics": [
        "computeMethylationDataCoverage"
      ]
    },
    {
      "page": "computeMethylationDataSpatialCorrelation",
      "title": "Compute methylation data spatial correlation",
      "topics": [
        "computeMethylationDataSpatialCorrelation"
      ]
    },
    {
      "page": "computeMethylationProfile",
      "title": "Compute methylation profile",
      "topics": [
        "computeMethylationProfile"
      ]
    },
    {
      "page": "computeOverlapProfile",
      "title": "Compute Overlaps Profile",
      "topics": [
        "computeOverlapProfile"
      ]
    },
    {
      "page": "computePMDs",
      "title": "Compute PMDs",
      "topics": [
        "computePMDs"
      ]
    },
    {
      "page": "computeVMDs",
      "title": "Compute VMDs",
      "topics": [
        "computeVMDs"
      ]
    },
    {
      "page": "DMRcaller",
      "title": "Call Differentially Methylated Regions (DMRs) between two samples",
      "topics": [
        "DMRcaller-package",
        "DMRcaller"
      ]
    },
    {
      "page": "DMRsNoiseFilterCG",
      "title": "The DMRs between WT and met1-3 in CG context",
      "topics": [
        "DMRsNoiseFilterCG"
      ]
    },
    {
      "page": "extractGC",
      "title": "Extract GC",
      "topics": [
        "extractGC"
      ]
    },
    {
      "page": "filterDMRs",
      "title": "Filter DMRs",
      "topics": [
        "filterDMRs"
      ]
    },
    {
      "page": "filterPMDs",
      "title": "Filter PMDs",
      "topics": [
        "filterPMDs"
      ]
    },
    {
      "page": "filterVMDs",
      "title": "Filter VMDs",
      "topics": [
        "filterVMDs"
      ]
    },
    {
      "page": "filterVMRsONT",
      "title": "Filter VMRs for ONT Data",
      "topics": [
        "filterVMRsONT"
      ]
    },
    {
      "page": "GEs",
      "title": "The genetic elements data",
      "topics": [
        "GEs"
      ]
    },
    {
      "page": "GEs_hg38",
      "title": "The genetic elements data of GRCh38 Genome Reference",
      "topics": [
        "GEs_hg38"
      ]
    },
    {
      "page": "getWholeChromosomes",
      "title": "Get whole chromosomes from methylation data",
      "topics": [
        "getWholeChromosomes"
      ]
    },
    {
      "page": "joinReplicates",
      "title": "Joins together two GRange objects in a single containing all the replicates",
      "topics": [
        "joinReplicates"
      ]
    },
    {
      "page": "mergeDMRsIteratively",
      "title": "Merge DMRs iteratively",
      "topics": [
        "mergeDMRsIteratively"
      ]
    },
    {
      "page": "mergePMDsIteratively",
      "title": "Merge PMDs iteratively",
      "topics": [
        "mergePMDsIteratively"
      ]
    },
    {
      "page": "methylationDataList",
      "title": "The methylation data list",
      "topics": [
        "methylationDataList"
      ]
    },
    {
      "page": "ont_gr_GM18870_chr1_PMD_bins_1k",
      "title": "Partially Methilated Domains example",
      "topics": [
        "ont_gr_GM18870_chr1_PMD_bins_1k"
      ]
    },
    {
      "page": "ont_gr_GM18870_chr1_sorted_bins_1k",
      "title": "The ONT methylation data example",
      "topics": [
        "ont_gr_GM18870_chr1_sorted_bins_1k"
      ]
    },
    {
      "page": "ontSampleGRangesList",
      "title": "The ONT methylation data list",
      "topics": [
        "ontSampleGRangesList"
      ]
    },
    {
      "page": "plotLocalMethylationProfile",
      "title": "Plot local methylation profile",
      "topics": [
        "plotLocalMethylationProfile"
      ]
    },
    {
      "page": "plotMethylationDataCoverage",
      "title": "Plot methylation data coverage",
      "topics": [
        "plotMethylationDataCoverage"
      ]
    },
    {
      "page": "plotMethylationDataSpatialCorrelation",
      "title": "Plot methylation data spatial correlation",
      "topics": [
        "plotMethylationDataSpatialCorrelation"
      ]
    },
    {
      "page": "plotMethylationProfile",
      "title": "Plot Methylation Profile",
      "topics": [
        "plotMethylationProfile"
      ]
    },
    {
      "page": "plotMethylationProfileFromData",
      "title": "Plot methylation profile from data",
      "topics": [
        "plotMethylationProfileFromData"
      ]
    },
    {
      "page": "plotOverlapProfile",
      "title": "Plot overlap profile",
      "topics": [
        "plotOverlapProfile"
      ]
    },
    {
      "page": "PMDsBinsCG",
      "title": "The PMDs between GM18501 and GM18876 using Bins method",
      "topics": [
        "PMDsBinsCG"
      ]
    },
    {
      "page": "PMDsNoiseFilterCG",
      "title": "The PMDs between GM18501 and GM18876 using Noise_filter method",
      "topics": [
        "PMDsNoiseFilterCG"
      ]
    },
    {
      "page": "poolMethylationDatasets",
      "title": "Pool methylation data",
      "topics": [
        "poolMethylationDatasets"
      ]
    },
    {
      "page": "poolTwoMethylationDatasets",
      "title": "Pool two methylation datasets",
      "topics": [
        "poolTwoMethylationDatasets"
      ]
    },
    {
      "page": "readBismark",
      "title": "Read Bismark",
      "topics": [
        "readBismark"
      ]
    },
    {
      "page": "readBismarkPool",
      "title": "Read Bismark pool",
      "topics": [
        "readBismarkPool"
      ]
    },
    {
      "page": "readONTbam",
      "title": "Load ONT BAM, decode MM/ML, and count modified vs. unmodified reads",
      "topics": [
        "readONTbam"
      ]
    },
    {
      "page": "saveBismark",
      "title": "Save Bismark",
      "topics": [
        "saveBismark"
      ]
    },
    {
      "page": "scanBamChr1Random5",
      "title": "The bam file from ONT nanopore .pod5 files",
      "topics": [
        "scanBamChr1Random5"
      ]
    },
    {
      "page": "selectCytosine",
      "title": "Select Cytosine Positions",
      "topics": [
        "selectCytosine"
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    },
    {
      "page": "syntheticDataReplicates",
      "title": "Simulated data for biological replicates",
      "topics": [
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  "_vignettes": [
    {
      "source": "DMRcaller.Rmd",
      "filename": "DMRcaller.html",
      "title": "Overview of the DMRcaller package",
      "author": "Nicolae Radu Zabet\\thanks{e-mail: \\texttt{r.zabet@qmul.ac.uk}, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK}",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Methods",
        "Description",
        "Data",
        "Bisulfite sequencing data",
        "Oxford Nanopore methylation data",
        "Oxford Nanopore cytosine reference selection",
        "Reading Oxford Nanopore BAM files",
        "Low resolution profiles",
        "Coverage of the bisulfite sequencing data",
        "Spatial correlation of methylation levels",
        "Calling DMRs",
        "Merge DMRs",
        "Calling DMRs using biological replicates",
        "Extract methylation data in regions",
        "Calling partially methylated domains (PMDs)",
        "Calling variably methylated domains (VMDs) using ONT data",
        "Detecting Variably Methylated Regions (VMRs) using ONT data",
        "Calling Co-Methylated Positions (CMPs) using ONT data",
        "Calling Co-Methylated Regions (CMRs) using ONT Data",
        "Plotting the distribution of DMRs, PMDs, VMDs or VMRs",
        "Plotting profiles with DMRs, PMDs, VMDs or VMRs",
        "Parallel computation",
        "Session information",
        "References"
      ],
      "created": "2025-09-03 16:29:10",
      "modified": "2025-10-17 13:51:50",
      "commits": 5
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