{
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  "Package": "consensusRegions",
  "Type": "Package",
  "Title": "Consensus Regions from Replicated ChIP-seq and ATAC-seq\nExperiments",
  "Version": "0.99.2",
  "Authors@R": "person(\"Sebastian\", \"Gregoricchio\",\nemail = \"s.gregoricchio@nki.nl\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9209-5403\"))",
  "Description": "Merges the evidence carried by replicated ChIP-seq,\nATAC-seq or CUT&RUN experiments into a single set of consensus\nregions. When several replicates agree on a position their\np-values are combined, so that a peak too weak to survive on\nits own can still be retained. Fisher, Stouffer, Lancaster and\nrank-product combinations are available; the weighted ones\naccept per-replicate weights taken from FRiP scores, library\nsizes, or the peak sets themselves when no alignment file is at\nhand. Input can be anything from a full narrowPeak to a bare\nBED3: scores are rank-transformed when p-values are missing,\nand a weighted k-of-n presence rule takes over when even the\nscore is absent. The threshold on the combined significance can\nbe calibrated against a permutation null rather than fixed a\npriori. Quality control plots and export to\nSummarizedExperiment are included.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "biocViews": "ChIPSeq, ATACSeq, PeakDetection, Epigenetics, Sequencing,\nQualityControl, MultipleComparison, Software",
  "URL": "https://github.com/sebastian-gregoricchio/consensusRegions",
  "BugReports": "https://github.com/sebastian-gregoricchio/consensusRegions/issues",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Collate": "'consensusRegions-package.R' 'AllClasses.R' 'AllGenerics.R'\n'utils.R' 'combineEvidence.R' 'readPeakSets.R'\n'computeReplicateWeights.R' 'buildConsensus.R'\n'calibrateThreshold.R' 'runConsensus.R' 'recentrePeaks.R'\n'exportConsensus.R' 'asSummarizedExperiment.R'\n'methods-ConsensusRegions.R' 'plots.R'",
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  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-10-08 17:29:10 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/consensusRegions",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-08 20:33:49 UTC",
    "User": "root"
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  "Author": "Sebastian Gregoricchio [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9209-5403>)",
  "Maintainer": "Sebastian Gregoricchio <s.gregoricchio@nki.nl>",
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  "_published": "2026-10-08T22:13:54.168Z",
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  "_host": "GitHub-Actions",
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    "id": "381aadb6a7429acdf28263a50ffe59ccffcd856e",
    "author": "Sebastian Gregoricchio <sebastian.gregoricchio@gmail.com>",
    "committer": "Sebastian Gregoricchio <sebastian.gregoricchio@gmail.com>",
    "message": "Improve Reproducibility\n\n* `calibrateThreshold()` and `runConsensus()` take `seed`, which seeds the\n  random positions of the shuffled peaks. It goes to the `BiocParallel`\n  backend built from `BPPARAM` as its `RNGseed`, so the same seed returns\n  the same threshold on one core or on many, and the random numbers of\n  the session are left as they were. The calibration keeps the `seed` and\n  its `seedSource`, and the object prints it.\n* The documentation said that `set.seed()` before the call brought the\n  same threshold back on a single core. It does not: `BiocParallel` draws\n  from random numbers of its own, which `set.seed()` does not reach, so\n  two identical calls could calibrate two different thresholds. The\n  examples, the vignette and the tests use `seed` now. A\n  `BiocParallelParam` passed as `BPPARAM` is still used untouched, and\n  carries its own `RNGseed`; `seed` is ignored with it, with a warning.\n",
    "time": 1791480550
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  "_topics": [
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    "peakdetection",
    "epigenetics",
    "sequencing",
    "qualitycontrol",
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      "page": "asSummarizedExperiment",
      "title": "Hand the consensus over to a differential analysis",
      "topics": [
        "asSummarizedExperiment"
      ]
    },
    {
      "page": "buildConsensus",
      "title": "Build consensus regions from replicated peak calls",
      "topics": [
        "buildConsensus"
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    },
    {
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      "title": "Calibrate the combined significance threshold",
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    },
    {
      "page": "combineEvidence",
      "title": "Combine the evidence carried by overlapping peaks",
      "topics": [
        "combineEvidence"
      ]
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    {
      "page": "computeReplicateWeights",
      "title": "Derive per-replicate weights",
      "topics": [
        "computeReplicateWeights"
      ]
    },
    {
      "page": "ConsensusRegions-accessors",
      "title": "Accessors for ConsensusRegions objects",
      "topics": [
        "analysisParameters",
        "analysisParameters,ConsensusRegions-method",
        "consensusRanges",
        "consensusRanges,ConsensusRegions-method",
        "ConsensusRegions-accessors",
        "consensusStats",
        "consensusStats,ConsensusRegions-method",
        "peakSets",
        "peakSets,ConsensusRegions-method",
        "replicateWeights",
        "replicateWeights,ConsensusRegions-method"
      ]
    },
    {
      "page": "ConsensusRegions-class",
      "title": "ConsensusRegions class",
      "topics": [
        "ConsensusRegions-class"
      ]
    },
    {
      "page": "exportConsensus",
      "title": "Write the results to disk",
      "topics": [
        "exportConsensus"
      ]
    },
    {
      "page": "ConsensusRegions-length",
      "title": "Number of consensus regions",
      "topics": [
        "length,ConsensusRegions-method"
      ]
    },
    {
      "page": "plotCalibration",
      "title": "The calibration curve",
      "topics": [
        "plotCalibration"
      ]
    },
    {
      "page": "plotJaccard",
      "title": "Pairwise agreement between replicates",
      "topics": [
        "plotJaccard"
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    },
    {
      "page": "plotRescue",
      "title": "Rescue and discard rates per replicate",
      "topics": [
        "plotRescue"
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    },
    {
      "page": "plotUpset",
      "title": "Which replicates contribute to each consensus region",
      "topics": [
        "plotUpset"
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      "page": "readPeakSets",
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      "topics": [
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    },
    {
      "page": "recentrePeaks",
      "title": "Recover summits and return fixed-width regions",
      "topics": [
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    },
    {
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      "topics": [
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    },
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      "topics": [
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      ]
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