design

Function names, signatures, and return values

The function names, arguments, and return values come from the biomaRt package, as this package is aiming to be a drop-in replacement for biomaRt.

Some arguments are no longer required, and are subsumed into the ellipsis (...) argument. For example, the mart argument is no longer required, as the connection to the database is handled internally by the package.

FAQ

Why a new package?

Two main reasons:

  • Both packages can co-exist for a while, so we can start the migration even if all use cases are not yet supported by remart.
  • While Ensembl is moving away from BioMart for newer releases:
    • Older releases remain available, and are still accessible via BioMart.
    • BioMart is an open-source project that is also used by other databases. remart is only providing access to Ensembl.

There is thus value in keeping the biomaRt package alive to address more complex edge cases, and external Mart databases, while remart can provide a drop-in replacement for newer Ensembl releases.