# Gene-Cluster Discovery, Annotation and Visualization

## Documentation for package ‘gclink’ version 1.1

- DESCRIPTION file
- Package README

## Help Pages

blastp_df | BLASTP Results for test Proteins
eggnog_df | EggNOG Functional Annotation Results
gclink | Gene-Cluster Discovery, Annotation and Visualization
gc_add | Complete Gene Clusters by Adding Missing ORFs
gc_cal | Identify and Extract Gene Clusters from Scaled BLAST Data
gc_cluster | Identify Breakpoints of Gene Clusters within a Contig
gc_plot | Plot Scaled Gene Clusters with Arrows
gc_position | Extract ORF Positions for One Specific Gene Cluster
gc_range | Determine ORF Range for a Candidate Gene Cluster
gc_scale | Scale Gene-Cluster Coordinates for Visualization
KO_group | KEGG Orthology (KO) Group Classification
length_filter | Remove Length Outliers from BLAST Results
orf_extract | Extract ORF and Genome Information from BLAST or BLASTP Results
orf_locate | Parse ORF Coordinates from Prodigal FASTA Headers
PGC_group | Photosynthesis Gene Classification Groups
photosynthesis_gene_list | Photosynthesis Gene List
seq_data | Genomic Sequence Data with Annotations