This functions retrieves details about the assembly of a queried species.
get_assemblies( species_name = "homo_sapiens", verbose = FALSE, warnings = TRUE, progress_bar = TRUE )
| species_name | The species name, i.e., the scientific name, all letters
lowercase and space replaced by underscore. Examples: |
|---|---|
| verbose | Whether to be chatty. |
| warnings | Whether to print warnings. |
| progress_bar | Whether to show a progress bar. |
A tibble, each row being a toplevel sequence,
of 4 variables:
species_nameEnsembl 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_nameAssembly name.
assembly_dateAssembly date.
genebuild_methodAnnotation method.
golden_path_lengthGolden path length.
genebuild_initial_release_dateGenebuild release date.
default_coord_system_versionDefault coordinate system version.
assembly_accessionAssembly accession.
genebuild_start_dateGenebuild start date.
genebuild_last_geneset_updateGenebuild last geneset update.
# Get details about the human assembly get_assemblies()#> # A tibble: 1 × 10 #> species_name assembly_name assembly_date genebuild_method golden_path_length #> <chr> <chr> <chr> <chr> <dbl> #> 1 homo_sapiens GRCh38.p13 2013-12 full_genebuild 3096649726 #> # … with 5 more variables: genebuild_initial_release_date <chr>, #> # default_coord_system_version <chr>, assembly_accession <chr>, #> # genebuild_start_date <chr>, genebuild_last_geneset_update <chr># Get details about the Mouse and the Fruit Fly genomes get_assemblies(c('mus_musculus', 'drosophila_melanogaster'))#> # A tibble: 2 × 9 #> species_name assembly_name assembly_date genebuild_method golden_path_len… #> <chr> <chr> <chr> <chr> <dbl> #> 1 mus_musculus GRCm39 2020-06 full_genebuild 2728222451 #> 2 drosophila_mela… BDGP6.32 NA import 143726002 #> # … with 4 more variables: default_coord_system_version <chr>, #> # assembly_accession <chr>, genebuild_start_date <chr>, #> # genebuild_last_geneset_update <chr>