Package index • rplaza

All functions

get_annotation(): Extract gene annotation as a GRanges object

get_block_duplicates(): Get anchor pairs in intraspecies syntenic regions

get_descriptions(): Get short, one-line gene descriptions

get_family_assignments(): Get gene family assignments for all genes in a PLAZA instance

get_family_functions(): Get enriched functional terms in gene families of a PLAZA instance

get_functional_annotation(): Get mapping between alternative IDs

get_genome(): Load genome sequences as a DNAStringSet object

get_id_conversions(): Get mapping between alternative IDs

get_sequences(): Get sequences for genomic loci as a DNAStringSet object

get_tx2gene(): Get transcript-to-gene mapping

plaza_metadata: Metadata and taxonomic information for all species on PLAZA instances

plaza_tree: Phylogenetic tree with relationships between species in all PLAZA instances