https://liuyanglee.r-universe.devRecent package updates in liuyangleeR-universehttps://github.com/liuyanglee.pnghttps://liuyanglee.r-universe.devMon, 20 Jul 2026 07:17:02 GMTcyanobacteria@yeah.net (Liuyang Li)Provides tools for analyzing metabolic pathway completeness, abundance, and transcripts using KEGG Orthology (KO) data from (meta)genomic and (meta)transcriptomic studies. Supports both completeness (presence/absence) and abundance-weighted analyses. Includes built-in KEGG reference datasets. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.https://github.com/r-universe/liuyanglee/actions/runs/29731297466Mon, 20 Jul 2026 07:17:02 GMTmclink1.1.2successhttps://liuyanglee.r-universe.devhttps://github.com/liuyanglee/mclinkcyanobacteria@yeah.net (Liuyang Li)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>.https://github.com/r-universe/liuyanglee/actions/runs/29319008723Wed, 03 Sep 2025 14:30:30 GMTgclink1.1successhttps://liuyanglee.r-universe.devhttps://github.com/liuyanglee/gclink