get_assemblies: Get details about the genome assembly of a species

In ramiromagno/ensemblr: R Client for the Ensembl REST API

Get details about the genome assembly of a species

Description

This functions retrieves details about the assembly of a queried species.

Usage

get_assemblies(
  species_name = "homo_sapiens",
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Arguments

species_name	The species name, i.e., the scientific name, all letters lowercase and space replaced by underscore. Examples: 'homo_sapiens' (human), 'ovis_aries' (Domestic sheep) or 'capra_hircus' (Goat).
verbose	Whether to be chatty.
warnings	Whether to print warnings.
progress_bar	Whether to show a progress bar.

Value

A tibble, each row being a toplevel sequence, of 4 variables:

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'.

assembly_name

Assembly name.

assembly_date

Assembly date.

genebuild_method

Annotation method.

golden_path_length

Golden path length.

genebuild_initial_release_date

Genebuild release date.

default_coord_system_version

Default coordinate system version.

assembly_accession

Assembly accession.

genebuild_start_date

Genebuild start date.

genebuild_last_geneset_update

Genebuild last geneset update.

Examples

# Get details about the human assembly
get_assemblies()

# Get details about the Mouse and the Fruit Fly genomes
get_assemblies(c('mus_musculus', 'drosophila_melanogaster'))

ramiromagno/ensemblr documentation built on Oct. 19, 2023, 11:12 a.m.