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 (>= 4.4.0)
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
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:37:12 UTC
RemoteUrl: https://github.com/bioc/linkSet
RemoteRef: HEAD
RemoteSha: bdadbdd362b9f200e14b5a7e144a7d13dd6a1881
NeedsCompilation: no
Packaged: 2026-01-09 21:45:45 UTC; root
Author: Gilbert Han [aut, cre] (ORCID: <https://orcid.org/0009-0000-0293-2467>)
Maintainer: Gilbert Han <GilbertHan1011@gmail.com>
Built: R 4.6.0; ; 2026-01-09 23:01:40 UTC; unix
