{
  "_id": "6a1fe3a7b401979e7343ac78",
  "Package": "BaalChIP",
  "Title": "BaalChIP: Bayesian analysis of allele-specific transcription\nfactor binding in cancer genomes",
  "Description": "The package offers functions to process multiple ChIP-seq\nBAM files and detect allele-specific events. Computes allele\ncounts at individual variants (SNPs/SNVs), implements extensive\nQC steps to remove problematic variants, and utilizes a\nbayesian framework to identify statistically significant\nallele- specific events. BaalChIP is able to account for copy\nnumber differences between the two alleles, a known\nphenotypical feature of cancer samples.",
  "Version": "1.39.0",
  "Author": "Ines de Santiago, Wei Liu, Ke Yuan, Martin O'Reilly, Chandra SR\nChilamakuri, Bruce Ponder, Kerstin Meyer, Florian Markowetz",
  "Maintainer": "Ines de Santiago <inesdesantiago@gmail.com>",
  "VignetteBuilder": "knitr",
  "License": "Artistic-2.0",
  "LazyData": "true",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:44:13 UTC",
  "RemoteUrl": "https://github.com/bioc/BaalChIP",
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    "User": "root"
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    "BaalChIP.get",
    "BaalChIP.report",
    "BaalChIP.run",
    "filter1allele",
    "filterIntbias",
    "getASB",
    "mergePerGroup",
    "plotQC",
    "plotSimul",
    "QCfilter",
    "summaryASB",
    "summaryQC"
  ],
  "_datasets": [
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      "name": "BaalObject",
      "title": "BaalObject example dataset",
      "object": "baalObject",
      "class": [
        "BaalChIP"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "title": "Blacklisted genomic regions",
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      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "title": "ENCODEexample example dataset",
      "object": "ENCODEexample",
      "class": [
        "BaalChIP"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
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      "title": "FAIREexample example dataset",
      "object": "FAIREexample",
      "class": [
        "BaalChIP"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "object": "pickrell2011cov1_hg19",
      "class": [
        "GRanges"
      ],
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      "table": false,
      "tojson": false
    },
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      "title": "Genomic regions of unique mappability",
      "object": "UniqueMappability50bp_hg19",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "adjustmentBaalPlot",
      "title": "Method adjustmentBaalPlot",
      "topics": [
        "adjustmentBaalPlot",
        "adjustmentBaalPlot,BaalChIP-method"
      ]
    },
    {
      "page": "alleleCounts",
      "title": "Method alleleCounts",
      "topics": [
        "alleleCounts",
        "alleleCounts,BaalChIP-method"
      ]
    },
    {
      "page": "BaalChIP",
      "title": "BaalChIP-class",
      "topics": [
        "BaalChIP"
      ]
    },
    {
      "page": "BaalChIP.get",
      "title": "Method BaalChIP.get",
      "topics": [
        "BaalChIP.get",
        "BaalChIP.get,BaalChIP-method"
      ]
    },
    {
      "page": "BaalChIP.report",
      "title": "Method BaalChIP.report",
      "topics": [
        "BaalChIP.report",
        "BaalChIP.report,BaalChIP-method"
      ]
    },
    {
      "page": "BaalChIP.run",
      "title": "Method BaalChIP.run",
      "topics": [
        "BaalChIP.run",
        "BaalChIP.run,BaalChIP-method"
      ]
    },
    {
      "page": "BaalObject",
      "title": "BaalObject example dataset",
      "topics": [
        "BaalObject"
      ]
    },
    {
      "page": "blacklist_hg19",
      "title": "Blacklisted genomic regions",
      "topics": [
        "blacklist_hg19"
      ]
    },
    {
      "page": "ENCODEexample",
      "title": "ENCODEexample example dataset",
      "topics": [
        "ENCODEexample"
      ]
    },
    {
      "page": "FAIREexample",
      "title": "FAIREexample example dataset",
      "topics": [
        "FAIREexample"
      ]
    },
    {
      "page": "filter1allele",
      "title": "Method filter1allele",
      "topics": [
        "filter1allele",
        "filter1allele,BaalChIP-method"
      ]
    },
    {
      "page": "filterIntbias",
      "title": "Method filterIntbias",
      "topics": [
        "filterIntbias",
        "filterIntbias,BaalChIP-method"
      ]
    },
    {
      "page": "getASB",
      "title": "Method getASB",
      "topics": [
        "getASB",
        "getASB,BaalChIP-method"
      ]
    },
    {
      "page": "mergePerGroup",
      "title": "Method mergePerGroup",
      "topics": [
        "mergePerGroup",
        "mergePerGroup,BaalChIP-method"
      ]
    },
    {
      "page": "pickrell2011cov1_hg19",
      "title": "Genomic regions of collapsed repeats",
      "topics": [
        "pickrell2011cov1_hg19"
      ]
    },
    {
      "page": "plotQC",
      "title": "Method plotQC",
      "topics": [
        "plotQC",
        "plotQC,BaalChIP-method"
      ]
    },
    {
      "page": "plotSimul",
      "title": "Method plotSimul",
      "topics": [
        "plotSimul",
        "plotSimul,BaalChIP-method"
      ]
    },
    {
      "page": "QCfilter",
      "title": "Method QCfilter",
      "topics": [
        "QCfilter",
        "QCfilter,BaalChIP-method"
      ]
    },
    {
      "page": "summaryASB",
      "title": "Method summaryASB",
      "topics": [
        "summaryASB",
        "summaryASB,BaalChIP-method"
      ]
    },
    {
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      "title": "Method summaryQC",
      "topics": [
        "summaryQC",
        "summaryQC,BaalChIP-method"
      ]
    },
    {
      "page": "UniqueMappability50bp_hg19",
      "title": "Genomic regions of unique mappability",
      "topics": [
        "UniqueMappability50bp_hg19"
      ]
    }
  ],
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      "source": "BaalChIP.Rmd",
      "filename": "BaalChIP.html",
      "title": "BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes",
      "author": " Ines de Santiago, Wei Liu, Ke Yuan, Florian Markowetz. University of Cambridge, Cancer Research UK Cambridge Institute",
      "engine": "knitr::rmarkdown",
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        "Introduction",
        "Standard workflow",
        "Quick start: example 1 (with pre-computed RAF scores)",
        "Quick start: example 1 with more control over the input options",
        "Quick start: example 2 (with gDNA BAM files)",
        "Input data",
        "The sample sheet",
        "The hets files",
        "The gDNA BAM files",
        "Constructing a BaalChIP object",
        "Obtaining allele-specific counts for BAM files",
        "QCfilter: A filter to exclude SNPs in regions of known problematic read alignment",
        "filterIntbias: A simulation-based filtering to exclude SNPs with intrinsic bias",
        "skipScriptRun",
        "Merge allele counts per group",
        "Removing possible homozygous SNPs",
        "Identifying allele-specific binding events",
        "The reference mapping (RM) bias",
        "The relative allele frequency (RAF) bias",
        "Exporting the results",
        "BaalChIP.report",
        "Sumarizing and plotting data",
        "The ENCODE data set",
        "The FAIREseq data set",
        "summaryQC: summary of QC result.",
        "plotQC: Plot filtering results",
        "Plot simulation results",
        "Exporting the table of assayed SNPs and their allelic counts",
        "summaryASB function",
        "Allelic ratios density plot",
        "Retrieving the RM and RAF scores estimated by BaalChIP",
        "Exporting the final ASB results with BaalChIP.report",
        "Bugs/Feature requests",
        "Session Information",
        "References"
      ],
      "created": "2016-08-18 19:05:00",
      "modified": "2021-03-01 13:29:20",
      "commits": 13
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