Get EnsDb from Bioconductor

Usage

getEnsDb(organism, genomeBuild = NULL, release = NULL)

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.

Value

EnsDb.

Details

Primarily fetches EnsDb objects from AnnotationHub. For legacy GRCh37 genome build, loads EnsDb.Hsapiens.v75 data package.

Note

Updated 2023-12-20.

UCSC genome build remapping

Remaps UCSC genome build to Ensembl automatically, if necessary. For example, "hg38" remaps to "GRCh38" and "hg19" to "GRCh37".

Examples

## Current genome build and release.
object <- getEnsDb(organism = "Homo sapiens")
#> → Getting <EnsDb> from AnnotationHub 4.2.2 (2026-04-23).
#> ℹ "AH119325": Ensembl 113 EnsDb for Homo sapiens.
print(object)
#> EnsDb for Ensembl:
#> |Backend: SQLite
#> |Db type: EnsDb
#> |Type of Gene ID: Ensembl Gene ID
#> |Supporting package: ensembldb
#> |Db created by: ensembldb package from Bioconductor
#> |script_version: 0.3.10
#> |Creation time: Sat Oct 26 21:34:14 2024
#> |ensembl_version: 113
#> |ensembl_host: 127.0.0.1
#> |Organism: Homo sapiens
#> |taxonomy_id: 9606
#> |genome_build: GRCh38
#> |DBSCHEMAVERSION: 2.2
#> |common_name: human
#> |species: homo_sapiens
#> | No. of genes: 87726.
#> | No. of transcripts: 413674.
#> |Protein data available.

## Legacy GRCh37 genome build.
if (requireNamespace("EnsDb.Hsapiens.v75", quietly = TRUE)) {
    object <- getEnsDb(organism = "Homo sapiens", genomeBuild = "GRCh37")
    print(object)
}
#> → Getting <EnsDb> from EnsDb.Hsapiens.v75.
#> EnsDb for Ensembl:
#> |Backend: SQLite
#> |Db type: EnsDb
#> |Type of Gene ID: Ensembl Gene ID
#> |Supporting package: ensembldb
#> |Db created by: ensembldb package from Bioconductor
#> |script_version: 0.3.0
#> |Creation time: Thu May 18 09:15:45 2017
#> |ensembl_version: 75
#> |ensembl_host: localhost
#> |Organism: homo_sapiens
#> |taxonomy_id: 9606
#> |genome_build: GRCh37
#> |DBSCHEMAVERSION: 2.0
#> | No. of genes: 64102.
#> | No. of transcripts: 215647.
#> |Protein data available.