Package: gclink
Title: Gene-Cluster Discovery, Annotation and Visualization
Version: 1.1
Authors@R: 
    person(given = "Liuyang",
           family = "Li",
           email = "cyanobacteria@yeah.net",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-6004-9437"))
Description: Performs end-to-end analysis of gene clusters—such as
        photosynthesis, carbon/nitrogen/sulfur cycling, carotenoid,
        antibiotic, or viral marker genes (e.g., capsid, polymerase,
        integrase)—from genomes and metagenomes. It parses Basic Local
        Alignment Search Tool (BLAST) results in tab-delimited format
        produced by tools like NCBI BLAST+ and Diamond BLASTp, filters
        Open Reading Frames (ORFs) by length, detects contiguous
        clusters of reference genes, optionally extracts genomic
        coordinates, merges functional annotations, and generates
        publication-ready arrow plots. The package works seamlessly
        with or without the coding sequences input and skips plotting
        when no functional groups are found. For more details see Li et
        al. (2023) <doi:10.1038/s41467-023-42193-7>.
URL: https://github.com/LiuyangLee/gclink
BugReports: https://github.com/LiuyangLee/gclink/issues
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: dplyr (>= 1.1.4), gggenes (>= 0.5.1), ggplot2 (>= 3.5.2),
        utils
Depends: R (>= 3.5)
LazyData: false
Config/check/use_internal_tz: TRUE
NeedsCompilation: no
Packaged: 2026-07-14 08:45:53 UTC; root
Config/pak/sysreqs: libicu-dev libjpeg-dev libpng-dev libxml2-dev
        libssl-dev
Repository: https://liuyanglee.r-universe.dev
Date/Publication: 2025-09-03 14:30:30 UTC
RemoteUrl: https://github.com/liuyanglee/gclink
RemoteRef: HEAD
RemoteSha: e8f397166440b1affae66c32f35a34c92723a101
Author: Liuyang Li [aut, cre] (ORCID: <https://orcid.org/0000-0001-6004-9437>)
Maintainer: Liuyang Li <cyanobacteria@yeah.net>