lists the available BioMart databases hosted by Ensembl

This function returns a list of BioMart databases hosted by Ensembl. To establish a connection use the useEnsembl() function.

Usage

listEnsembl(
  mart = NULL,
  version = NULL,
  GRCh = NULL,
  mirror = NULL,
  verbose = FALSE
)

listEnsemblGenomes(includeHosts = FALSE, host = NULL)

Arguments

mart: mart object created with the useEnsembl function. This is optional, as you usually use listMarts() to see which marts there are to connect to.
version: Ensembl version to connect to when wanting to connect to an archived Ensembl version
GRCh: GRCh version to connect to if not the current GRCh38, currently this can only be 37
mirror: Specify an Ensembl mirror to connect to. The valid options here are 'www', 'useast', 'asia'. If no mirror is specified the primary site at www.ensembl.org will be used.
verbose: Give detailed output of what the method is doing, for debugging purposes
includeHosts: If this option is set to TRUE a more detailed output is produced, including the URL used to access the corresponding mart.
host: Host to connect to. Use this argument to specify and archive site for listEnsemblGenomes() to work with.

Author

Steffen Durinck, Mike L. Smith

Examples


if(interactive()){
listEnsembl()

## list the default Ensembl Genomes marts
listEnsemblGenomes()

## list only the marts available in the Ensmbl Plans 56 archive
listEnsemblGenomes(host = "https://eg56-plants.ensembl.org/")
}