Package: linkSet
Title: Base Classes for Storing Genomic Link Data
Version: 1.1.0
Authors@R: 
    c(person("Gilbert", "Han", , "GilbertHan1011@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0009-0000-0293-2467")))
Description: Provides a comprehensive framework for representing, analyzing, 
    and visualizing genomic interactions, particularly focusing on gene-enhancer
    relationships. The package extends the GenomicRanges infrastructure to handle
    paired genomic regions with specialized methods for chromatin interaction data
    from Hi-C, Promoter Capture Hi-C (PCHi-C), and single-cell ATAC-seq experiments.
    Key features include conversion from common interaction formats, annotation of
    promoters and enhancers, distance-based analyses, interaction strength metrics,
    statistical modeling using CHiCANE methodology, and tailored visualization tools.
    The package aims to standardize the representation of genomic interaction data
    while providing domain-specific functions not available in general genomic
    interaction packages.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: 
    GenomicRanges,
    S4Vectors,
    R (>= 4.5.0)
Imports: 
    methods,
    IRanges,
    GenomeInfoDb,
    BiocGenerics,
    Organism.dplyr,
    InteractionSet,
    ggplot2,
    patchwork,
    scales,
    foreach,
    iterators,
    stats,
    rlang,
    MASS,
    data.table,
    DBI,
    doParallel,
    AnnotationDbi
Suggests: 
    knitr,
    rmarkdown,
    testthat,
    TxDb.Mmusculus.UCSC.mm10.knownGene,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    org.Mm.eg.db,
    org.Hs.eg.db,
    GenomicFeatures,
    GenomicInteractions,
    gamlss,
    gamlss.tr,
    BiocStyle,
    rtracklayer
Collate: class.R AllGenerics.R getset.R
        methods.R annotate.R distance.R formatConverter.R 
        linkSet-package.R GRange_method.R test_helper.R
        visualization.R count.R statical.R data.R
biocViews: Software, HiC, DataRepresentation, Sequencing, SingleCell, Coverage
URL: https://github.com/GilbertHan1011/linkSet, https://gilberthan1011.github.io/linkSet
BugReports: https://github.com/GilbertHan1011/linkSet/issues/new
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/linkSet
git_branch: devel
git_last_commit: bdadbdd
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
