Package: epiPortrait
Type: Package
Title: Replicate-Aware Epigenomic Domain Profiling
Version: 0.99.3
Depends: R (>= 4.5.0)
Authors@R: c(
    person(given = "Ying", family = "ZHANG", 
           role = c("aut", "cre"), 
           email = "12207129@zju.edu.cn", 
           comment = c(ORCID = "0009-0005-9644-7062")),
    person(given = "Xingze", family = "HUANG",
           role = c("ctb"),
           email = "22407026@zju.edu.cn",
           comment = c(ORCID = "0009-0002-9286-1344")),
    person(given = "Ye", family = "CHEN",
           role = "ctb",
           email = "chenyephd@zju.edu.cn"),
    person(given = "Liang", family = "XU",
           role = c("ctb", "fnd"), 
           email = "xuliang.phd@zju.edu.cn",
           comment = "This work is funded by the Fundamental Research Funds for the Central Universities (226-2025-00101) and the National Natural Science Foundation of China (32270746, 82203247, 82203415).")
  )
Description: Provides methods for replicate-aware quantitative
        phenotyping and comparison of epigenomic domains from
        normalized continuous signal tracks and per-sample native
        peak/domain calls (histone-mark ChIP-seq / CUT&Tag as the
        primary use case; also applicable to ATAC-seq-derived domains).
        It characterizes each shared genomic domain by integrated
        signal magnitude (Intensity), sample-specific native peak
        breadth geometry, and continuous within-domain signal
        architecture (SignalDispersion). Replicate-level evidence is
        retained and aggregated with specified support rules, enabling
        condition-specific classification of Intensity-Super,
        Breadth-Super, Dual-Super, Typical, or Uncertain domain states
        without using the consensus-domain width as the breadth caller.
        The package further supports condition transitions, continuous
        domain-width remodeling, signal quality control, genome-aware
        domain annotation with a three-level export (per-domain
        summary, per-domain-gene pair, and raw relationship detail),
        optional BEDPE contact evidence, expression-aware
        candidate-gene prioritization, differential domain analysis on
        continuous BigWig signal using limma, and result visualization.
License: GPL (>= 3) + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
biocViews: ChIPSeq, ATACSeq, Epigenetics, Coverage, Normalization,
        DifferentialExpression, GenomeAnnotation, QualityControl,
        Visualization, PrincipalComponent
URL: https://github.com/zying106/epiPortrait
BugReports: https://github.com/zying106/epiPortrait/issues
Imports: digest, GenomeInfoDb, GenomicRanges, rtracklayer,
        SummarizedExperiment, BiocParallel, S4Vectors, IRanges,
        GenomicFeatures, ggplot2, scales, ggrepel, limma, methods,
        stats, AnnotationDbi, withr
Suggests: BiocStyle, edgeR, HDF5Array, knitr, org.Hs.eg.db,
        org.Mm.eg.db, ragg, rmarkdown, svglite, testthat, txdbmaker,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        TxDb.Mmusculus.UCSC.mm10.knownGene
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-04 00:02:14 UTC
RemoteUrl: https://github.com/BiocStaging/epiPortrait
RemoteRef: HEAD
RemoteSha: 6dd14984eba9dfb38708b30501b2edd85b6dcbf9
NeedsCompilation: no
Packaged: 2026-10-04 10:11:12 UTC; root
Author: Ying ZHANG [aut, cre] (ORCID: <https://orcid.org/0009-0005-9644-7062>),
  Xingze HUANG [ctb] (ORCID: <https://orcid.org/0009-0002-9286-1344>),
  Ye CHEN [ctb],
  Liang XU [ctb, fnd] (This work is funded by the Fundamental Research
    Funds for the Central Universities (226-2025-00101) and the
    National Natural Science Foundation of China (32270746, 82203247,
    82203415).)
Maintainer: Ying ZHANG <12207129@zju.edu.cn>