eggnog_df

A dataset containing EggNOG functional annotation results,
including taxonomic classification, functional categories, and domain information.

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

eggnog_df function

A data frame with multiple rows and 21 variables:<dl>
<dt>#query</dt>
<dd>Character. Protein query identifier (e.g., "Houyiibacteriaceae--LLY-WYZ-15_3---k141_356661_13").</dd><dt>seed_ortholog</dt>
<dd>Character. Subject protein identifier from EggNOG database (e.g., "1168065.DOK_14784").</dd><dt>evalue</dt>
<dd>Numeric. Expect value for the annotation.</dd><dt>score</dt>
<dd>Numeric. Annotation bitscore.</dd><dt>eggNOG_OGs</dt>
<dd>Character.</dd><dt>max_annot_lvl</dt>
<dd>Character.</dd><dt>COG_category</dt>
<dd>Character.</dd><dt>Description</dt>
<dd>Character. Functional description (e.g., "Bacterial regulatory proteins, tetR family").</dd><dt>Preferred_name</dt>
<dd>Character. Gene name if available (e.g., "cobB").</dd><dt>GOs</dt>
<dd>Character.</dd><dt>EC</dt>
<dd>Character. Enzyme Commission number if applicable (e.g., "2.7.7.49").</dd><dt>KEGG_ko</dt>
<dd>Character. KEGG Orthology identifier if available (e.g., "ko:K00986").</dd><dt>KEGG_Pathway</dt>
<dd>Character.</dd><dt>KEGG_Module</dt>
<dd>Character.</dd><dt>KEGG_Reaction</dt>
<dd>Character.</dd><dt>KEGG_rclass</dt>
<dd>Character.</dd><dt>BRITE</dt>
<dd>Character.</dd><dt>KEGG_TC</dt>
<dd>Character.</dd><dt>CAZy</dt>
<dd>Character.</dd><dt>BiGG_Reaction</dt>
<dd>Character.</dd><dt>PFAMs</dt>
<dd>Character.</dd>
</dl>

Format

EggNOG Functional Annotation Results — eggnog_df

A data frame with multiple rows and 21 variables:<dl>
<dt>#query</dt>
<dd>Character. Protein query identifier (e.g., "Houyiibacteriaceae--LLY-WYZ-15_3---k141_356661_13").</dd>

<dt>seed_ortholog</dt>
<dd>Character. Subject protein identifier from EggNOG database (e.g., "1168065.DOK_14784").</dd>

<dt>evalue</dt>
<dd>Numeric. Expect value for the annotation.</dd>

<dt>score</dt>
<dd>Numeric. Annotation bitscore.</dd>

<dt>eggNOG_OGs</dt>
<dd>Character.</dd>

<dt>max_annot_lvl</dt>
<dd>Character.</dd>

<dt>COG_category</dt>
<dd>Character.</dd>

<dt>Description</dt>
<dd>Character. Functional description (e.g., "Bacterial regulatory proteins, tetR family").</dd>

<dt>Preferred_name</dt>
<dd>Character. Gene name if available (e.g., "cobB").</dd>

<dt>GOs</dt>
<dd>Character.</dd>

<dt>EC</dt>
<dd>Character. Enzyme Commission number if applicable (e.g., "2.7.7.49").</dd>

<dt>KEGG_ko</dt>
<dd>Character. KEGG Orthology identifier if available (e.g., "ko:K00986").</dd>

<dt>KEGG_Pathway</dt>
<dd>Character.</dd>

<dt>KEGG_Module</dt>
<dd>Character.</dd>

<dt>KEGG_Reaction</dt>
<dd>Character.</dd>

<dt>KEGG_rclass</dt>
<dd>Character.</dd>

<dt>BRITE</dt>
<dd>Character.</dd>

<dt>KEGG_TC</dt>
<dd>Character.</dd>

<dt>CAZy</dt>
<dd>Character.</dd>

<dt>BiGG_Reaction</dt>
<dd>Character.</dd>

<dt>PFAMs</dt>
<dd>Character.</dd>


</dl>

eggnog_df: EggNOG Functional Annotation Results

Description

Usage

Arguments

Format