List resolvable genome names

Returns a data frame describing every genome resolvable from the active registry chain (see gdb.build_genome for the chain order).

Usage

gdb.list_genomes(registry = NULL)

Arguments

registry

Optional path to an explicit registry YAML, overriding the resolution chain.

Value

A data frame with columns:

• name - registry key.

• source - backend (ucsc, ncbi, s3, local, manual).

• detail - assembly / accession / path.

• resolved_from - which registry the entry came from.

See also

gdb.build_genome, gdb.genome_info.

Examples

gdb.list_genomes()
#>        name source   detail resolved_from
#> 1      hg19   ucsc     hg19      built-in
#> 2      hg38   ucsc     hg38      built-in
#> 3       mm9   ucsc      mm9      built-in
#> 4      mm10   ucsc     mm10      built-in
#> 5      mm39   ucsc     mm39      built-in
#> 6       rn6   ucsc      rn6      built-in
#> 7       rn7   ucsc      rn7      built-in
#> 8       dm6   ucsc      dm6      built-in
#> 9      ce11   ucsc     ce11      built-in
#> 10  sacCer3   ucsc  sacCer3      built-in
#> 11 danRer11   ucsc danRer11      built-in