Package: linkSet
Title: Base Classes for Storing Genomic Link Data
Version: 1.0.0
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: RELEASE_3_22
git_last_commit: e983433
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 04:45:09 UTC; biocbuild
Author: Gilbert Han [aut, cre] (ORCID: <https://orcid.org/0009-0000-0293-2467>)
Maintainer: Gilbert Han <GilbertHan1011@gmail.com>
