PGC_group

A dataset mapping photosynthesis-related genes to their functional groups and subunits.

datasets

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>.

Liuyang Li

gclink

Gene-Cluster Discovery, Annotation and Visualization

PGC_group function

A data frame with multiple rows and 3 variables:<dl>
<dt>gene</dt>
<dd>Character. Gene identifier (e.g., "bchB").</dd><dt>gene_group</dt>
<dd>Character. Functional group (e.g., "bch").</dd><dt>gene_label</dt>
<dd>Character. Subunit designation (e.g., "B").</dd>
</dl>

Format

Photosynthesis Gene Classification Groups — PGC_group

A data frame with multiple rows and 3 variables:<dl>
<dt>gene</dt>
<dd>Character. Gene identifier (e.g., "bchB").</dd>

<dt>gene_group</dt>
<dd>Character. Functional group (e.g., "bch").</dd>

<dt>gene_label</dt>
<dd>Character. Subunit designation (e.g., "B").</dd>


</dl>

PGC_group: Photosynthesis Gene Classification Groups

Description

Usage

Arguments

Format