Package: consensusRegions
Type: Package
Title: Consensus Regions from Replicated ChIP-seq and ATAC-seq
        Experiments
Version: 0.99.2
Authors@R: person("Sebastian", "Gregoricchio",
                  email = "s.gregoricchio@nki.nl",
                  role = c("aut", "cre"),
                  comment = c(ORCID = "0000-0001-9209-5403"))
Description: Merges the evidence carried by replicated ChIP-seq,
        ATAC-seq or CUT&RUN experiments into a single set of consensus
        regions. When several replicates agree on a position their
        p-values are combined, so that a peak too weak to survive on
        its own can still be retained. Fisher, Stouffer, Lancaster and
        rank-product combinations are available; the weighted ones
        accept per-replicate weights taken from FRiP scores, library
        sizes, or the peak sets themselves when no alignment file is at
        hand. Input can be anything from a full narrowPeak to a bare
        BED3: scores are rank-transformed when p-values are missing,
        and a weighted k-of-n presence rule takes over when even the
        score is absent. The threshold on the combined significance can
        be calibrated against a permutation null rather than fixed a
        priori. Quality control plots and export to
        SummarizedExperiment are included.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.5.0), GenomicRanges (>= 1.56.0)
Imports: BiocGenerics, BiocParallel, dplyr (>= 1.1.0), GenomeInfoDb,
        ggplot2, ggtext, grDevices, IRanges, methods, rlang, Rsamtools,
        rtracklayer, S4Vectors, stats, SummarizedExperiment, tibble,
        tidyr, tools
Suggests: BiocStyle, ComplexUpset, knitr, rmarkdown, testthat (>=
        3.0.0)
biocViews: ChIPSeq, ATACSeq, PeakDetection, Epigenetics, Sequencing,
        QualityControl, 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'
        'utils.R' 'combineEvidence.R' 'readPeakSets.R'
        'computeReplicateWeights.R' 'buildConsensus.R'
        'calibrateThreshold.R' 'runConsensus.R' 'recentrePeaks.R'
        'exportConsensus.R' 'asSummarizedExperiment.R'
        'methods-ConsensusRegions.R' 'plots.R'
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-08 17:29:10 UTC
RemoteUrl: https://github.com/BiocStaging/consensusRegions
RemoteRef: HEAD
RemoteSha: 381aadb6a7429acdf28263a50ffe59ccffcd856e
NeedsCompilation: no
Packaged: 2026-10-08 20:33:49 UTC; root
Author: Sebastian Gregoricchio [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9209-5403>)
Maintainer: Sebastian Gregoricchio <s.gregoricchio@nki.nl>