Get Ensembl species — get_species • ensemblr

This function retrieves species-level information. The data is returned as a tibble where each row is a species and the columns are metadata about each species. See below under section Value for details about each column.

Usage

get_species(
  division = get_divisions(),
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Arguments

division: Ensembl division, e.g., "EnsemblVertebrates" or "EnsemblBacteria", or a combination of several divisions. Check function get_divisions to get available Ensembl divisions.
verbose: Whether to be verbose about the http requests and respective responses' status.
warnings: Whether to show warnings.
progress_bar: Whether to show a progress bar.

Value

A tibble of 12 variables:

division: Ensembl division: "EnsemblVertebrates", "EnsemblMetazoa", "EnsemblPlants", "EnsemblProtists", "EnsemblFungi" or "EnsemblBacteria".
taxon_id: NCBI taxon identifier.
species_name: Ensembl species name: this is the name used internally by Ensembl to uniquely identify a species by name. It is the scientific name but formatted without capitalisation and spacing converted with an underscore, e.g., 'homo_sapiens'.
species_display_name: Species display name: the name used for display on Ensembl website.
species_common_name: Species common name.
release: Ensembl release version.
genome_assembly_name: Code name of the genome assembly.
genbank_assembly_accession: Genbank assembly accession identifier.
strain: Species strain.
strain_collection: Species strain collection.
species_aliases: Other names or acronyms used to refer to the species. Note that this column is of the list type.
groups: Ensembl databases for which data exists for this species. Note that this column is of the list type.