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gclink  

Gene-Cluster Discovery, Annotation and Visualization
View on CRAN: Click here


Download and install gclink package within the R console
Install from CRAN:
install.packages("gclink")

Install from Github:
library("remotes")
install_github("cran/gclink")

Install by package version:
library("remotes")
install_version("gclink", "1.1")



Attach the package and use:
library("gclink")
Maintained by
Liuyang Li
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2025-09-02
Latest Update: 2025-09-02
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>.
How to cite:
Liuyang Li (2025). gclink: Gene-Cluster Discovery, Annotation and Visualization. R package version 1.1, https://cran.r-project.org/web/packages/gclink. Accessed 26 Jun. 2026.
Previous versions and publish date:
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Complete documentation for gclink
Functions, R codes and Examples using the gclink R package
Full gclink package functions and examples
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