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
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: 2025-08-28 14:44:20 UTC; Administrator
Author: Liuyang Li [aut, cre] (ORCID: <https://orcid.org/0000-0001-6004-9437>)
Maintainer: Liuyang Li <cyanobacteria@yeah.net>
Repository: CRAN
Date/Publication: 2025-09-02 21:10:08 UTC
Built: R 4.6.0; ; 2026-01-05 18:59:15 UTC; windows
