Package: GPlinksR
Type: Package
Title: Building Gene-Peak Network for ATAC-RNA Integration
Version: 0.99.2
Authors@R: c(
    person(
        "Xinran", "Wang",
        email = "xwang210@usc.edu",
        role = c("aut", "cre"),
        comment = c(ORCID = "0009-0000-1805-3280")
    ),
    person("Kelly", "Street", email = "kelly.street@usc.edu", role = "ctb"),
    person("Huaiyu", "Mi", email = "huaiyumi@usc.edu", role = "ctb"),
    person("Bryan", "Queme", email = "queme@usc.edu", role = "ctb"))
Description: GPlinksR constructs gene-peak regulatory networks for
        ATAC-RNA integration by combining enhancer-based,
        promoter-based, and proximity (closest-gene) mappings. The
        package accepts direct peak and gene vectors as well as
        container-based inputs through a wrapper for common
        Bioconductor object classes. Enhancer-gene links are obtained
        from the PEREGRINE enhancer-gene datasets provided by AnnoQ,
        while promoter and gene coordinates are retrieved from
        EnsDb.Hsapiens.v86.
License: MIT + file LICENSE
URL: https://github.com/Corawang123/GPlinksR
BugReports: https://github.com/Corawang123/GPlinksR/issues
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: BiocFileCache, data.table, GenomicRanges, GenomeInfoDb,
        IRanges, methods, MultiAssayExperiment, S4Vectors,
        EnsDb.Hsapiens.v86, ensembldb, biomaRt, dplyr,
        SingleCellExperiment, SummarizedExperiment
biocViews: GeneExpression, Network, Sequencing, Transcriptomics
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
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: 2026-07-14 21:00:04 UTC
RemoteUrl: https://github.com/bioc/GPlinksR
RemoteRef: HEAD
RemoteSha: 6a7555bbae86bfc5e04abcd975f8b200a606efc2
NeedsCompilation: no
Packaged: 2026-09-30 07:41:25 UTC; root
Author: Xinran Wang [aut, cre] (ORCID: <https://orcid.org/0009-0000-1805-3280>),
  Kelly Street [ctb],
  Huaiyu Mi [ctb],
  Bryan Queme [ctb]
Maintainer: Xinran Wang <xwang210@usc.edu>