Download Ensembl reference genome

Usage

downloadEnsemblGenome(
  organism,
  genomeBuild = NULL,
  release = NULL,
  outputDir = getwd(),
  cache = FALSE
)

Arguments

organism: character(1). Full Latin organism name (e.g. "Homo sapiens").
genomeBuild: character(1). Ensembl genome build assembly name (e.g. "GRCh38"). If set NULL, defaults to the most recent build available. Note: don't pass in UCSC build IDs (e.g. "hg38").
release: integer(1). Ensembl release version (e.g. 100). We recommend setting this value if possible, for improved reproducibility. When left unset, the latest release available via AnnotationHub/ensembldb is used. Note that the latest version available can vary, depending on the versions of AnnotationHub and ensembldb in use.
outputDir: character(1). Output directory path.
cache: logical(1). Cache URLs locally, using BiocFileCache internally.

Value

Invisible list.

Note

Updated 2023-10-12.

Examples

## This example is bandwidth intensive.
## > downloadEnsemblGenome(
## >     organism = "Homo sapiens",
## >     genomeBuild = "GRCh38",
## >     release = 100L
## > )