gclink: Gene-Cluster Discovery, Annotation and Visualization

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>.

Version:	1.1
Depends:	R (≥ 3.5)
Imports:	dplyr (≥ 1.1.4), gggenes (≥ 0.5.1), ggplot2 (≥ 3.5.2), utils
Published:	2025-09-02
DOI:	10.32614/CRAN.package.gclink
Author:	Liuyang Li [aut, cre]
Maintainer:	Liuyang Li <cyanobacteria at yeah.net>
BugReports:	https://github.com/LiuyangLee/gclink/issues
License:	GPL-3
URL:	https://github.com/LiuyangLee/gclink
NeedsCompilation:	no
Materials:	README
CRAN checks:	gclink results

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