{
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  "Package": "DiffBind",
  "Type": "Package",
  "Version": "3.23.3",
  "Title": "Differential Binding Analysis of ChIP-Seq Peak Data",
  "Authors@R": "c(person(\"Rory\",\"Stark\", email=\"bioconductor@starkhome.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Gord\",\"Brown\",email=\"DECEASED\",\nrole=\"aut\"))",
  "Description": "Compute differentially bound sites from multiple ChIP-seq\nexperiments using affinity (quantitative) data. Also enables\noccupancy (overlap) analysis and plotting functions.",
  "License": "Artistic-2.0",
  "LazyLoad": "yes",
  "SystemRequirements": "GNU make",
  "Collate": "core.R parallel.R model.R counts.R contrast.R normalize.R\nanalyze.R analyze_deseq2.R analyze_edgeR.R blacklist.R report.R\nplots.R plotProfile.R io.R helper.R utils.R RcppExports.R\ncpp_wrapper.R DBA.R",
  "biocViews": "Sequencing, ChIPSeq,ATACSeq, DNaseSeq, MethylSeq, RIPSeq,\nDifferentialPeakCalling, DifferentialMethylation,\nGeneRegulation, HistoneModification, PeakDetection,\nBiomedicalInformatics, CellBiology, MultipleComparison,\nNormalization, ReportWriting, Epigenetics, FunctionalGenomics",
  "URL": "https://bioconductor.org/packages/DiffBind/",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-07-01 18:22:37 UTC",
  "RemoteUrl": "https://github.com/bioc/DiffBind",
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  "Packaged": {
    "Date": "2026-07-05 13:59:44 UTC",
    "User": "root"
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  "Author": "Rory Stark [aut, cre],\nGord Brown [aut]",
  "Maintainer": "Rory Stark <bioconductor@starkhome.com>",
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  "_created": "2026-07-05T13:59:44.000Z",
  "_published": "2026-07-05T14:14:31.747Z",
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    "warning": 4,
    "note": 19
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    "id": "a26ef8d38fc02a6865093d58d3636dc531a1fbb8",
    "author": "Rory Stark <bioconductor@starkhome.com>",
    "committer": "Rory Stark <bioconductor@starkhome.com>",
    "message": "3.23.3: preserve bSubControl set in dba.count()\n\ndba.count(bSubControl=) was recorded on the input object in\npv.counts() but dropped when the counted object was rebuilt by\npv.vectors(), so the returned DBA had $bSubControl = NULL. A\nsubsequent dba.normalize()/dba.analyze() then fell back to\nis.null(greylist), silently subtracting control reads regardless\nof the user's choice.\n\npv.counts() now re-stamps bSubControl onto the reconstructed\nobject (alongside minCount) and forwards it through the summit\nre-centering recursion. Default behavior (no explicit\nbSubControl) is unchanged.\n\nReported by Tomasz Wlodarczyk and Xiaosai Yao.\n",
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    "DBA_READS",
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    "DBA_READS_DEFAULT",
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    "DBA_SCORE_CONC_DENOMINATOR",
    "DBA_SCORE_CONC_NUMERATOR",
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    "DBA_SCORE_CONTROL_READS",
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    "DBA_SCORE_PVAL",
    "DBA_SCORE_READS",
    "DBA_SCORE_READS_EFFECTIVE",
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    "DBA_SCORE_RPKM_FOLD",
    "DBA_SCORE_RPKM_MINUS",
    "DBA_SCORE_SUMMIT",
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      "title": "Tamoxifen resistance dataset used for DBA examples",
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  "_help": [
    {
      "page": "DiffBind-package",
      "title": "Differential Binding Analysis of ChIP-seq peaksets",
      "topics": [
        "DiffBind-package",
        "DiffBind"
      ]
    },
    {
      "page": "dba",
      "title": "Construct a DBA object",
      "topics": [
        "dba"
      ]
    },
    {
      "page": "print.DBA",
      "title": "Standard S3 methods for DBA object",
      "topics": [
        "DBA-config",
        "DBA-object",
        "DBA.config",
        "DBA.object",
        "DiffBind-config",
        "DiffBind.config",
        "plot.DBA",
        "print.DBA",
        "summary.DBA"
      ]
    },
    {
      "page": "tamoxifen",
      "title": "Tamoxifen resistance dataset used for DBA examples",
      "topics": [
        "tamoxifen",
        "tamoxifen.greylist",
        "tamoxifen_analysis",
        "tamoxifen_counts",
        "tamoxifen_greylist",
        "tamoxifen_peaks"
      ]
    },
    {
      "page": "dba.analyze",
      "title": "Perform differential binding affinity analysis",
      "topics": [
        "dba.analyze"
      ]
    },
    {
      "page": "dba.blacklist",
      "title": "Apply blacklists and/or greylists to peaks (and generate greylist)",
      "topics": [
        "dba.blacklist"
      ]
    },
    {
      "page": "dba.contrast",
      "title": "Set up contrasts for differential binding affinity analysis",
      "topics": [
        "dba.contrast"
      ]
    },
    {
      "page": "dba.count",
      "title": "Count reads in binding site intervals",
      "topics": [
        "dba.count"
      ]
    },
    {
      "page": "dba.load",
      "title": "load DBA object",
      "topics": [
        "dba.load"
      ]
    },
    {
      "page": "dba.mask",
      "title": "Derive a mask to define a subset of peaksets or sites for a DBA object",
      "topics": [
        "dba.mask"
      ]
    },
    {
      "page": "dba.normalize",
      "title": "Specify parameters for normalizing a dataset; calculate library sizes and normalization factors.",
      "topics": [
        "dba.normalize"
      ]
    },
    {
      "page": "dba.overlap",
      "title": "Compute binding site overlaps (occupancy analysis)",
      "topics": [
        "dba.overlap"
      ]
    },
    {
      "page": "dba.peakset",
      "title": "Add a peakset to, or retrieve a peakset from, a DBA object",
      "topics": [
        "dba.peakset"
      ]
    },
    {
      "page": "dba.plotBox",
      "title": "Boxplots",
      "topics": [
        "dba.plotBox"
      ]
    },
    {
      "page": "dba.plotHeatmap",
      "title": "Draw a binding site heatmap",
      "topics": [
        "dba.plotHeatmap"
      ]
    },
    {
      "page": "dba.plotMA",
      "title": "Generate MA and scatter plots of differential binding analysis results",
      "topics": [
        "dba.plotMA"
      ]
    },
    {
      "page": "dba.plotPCA",
      "title": "PCA plot",
      "topics": [
        "dba.plotPCA"
      ]
    },
    {
      "page": "dba.plotProfile",
      "title": "Generate profiles and make profile heatmaps",
      "topics": [
        "dba.plotProfile"
      ]
    },
    {
      "page": "dba.plotVenn",
      "title": "Draw 2-way, 3-way, or 4-way Venn diagrams of overlaps",
      "topics": [
        "dba.plotVenn"
      ]
    },
    {
      "page": "dba.plotVolcano",
      "title": "Generate volcano plots of differential binding analysis results",
      "topics": [
        "dba.plotVolcano"
      ]
    },
    {
      "page": "dba.report",
      "title": "Generate a report for a differential binding affinity analysis",
      "topics": [
        "dba.report"
      ]
    },
    {
      "page": "dba.save",
      "title": "save DBA object",
      "topics": [
        "dba.save"
      ]
    },
    {
      "page": "dba.show",
      "title": "List attributes of peaksets of contrasts associated with a DBA object",
      "topics": [
        "dba.show"
      ]
    },
    {
      "page": "DiffBind-globals",
      "title": "Constant variables used in DiffBind package",
      "topics": [
        "DBA_ALL_ATTRIBUTES",
        "DBA_ALL_BLOCK",
        "DBA_ALL_METHODS",
        "DBA_ALL_METHODS_BLOCK",
        "DBA_BLACKLIST",
        "DBA_BLACKLISTED_PEAKS",
        "DBA_BLACKLIST_CE10",
        "DBA_BLACKLIST_CE11",
        "DBA_BLACKLIST_DM3",
        "DBA_BLACKLIST_DM6",
        "DBA_BLACKLIST_GRCH37",
        "DBA_BLACKLIST_GRCH38",
        "DBA_BLACKLIST_HG19",
        "DBA_BLACKLIST_HG38",
        "DBA_BLACKLIST_MM10",
        "DBA_BLACKLIST_MM9",
        "DBA_CALLER",
        "DBA_CONDITION",
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