Comparison between remart and biomaRt

12 October 2026

While we tried as much as possible to reproduce the biomaRt interface, there are some differences between the two packages, and limitations that we won’t be able to overcome.

Interface

New species / speciesL argument

In biomaRt, the mart argument was used to specify the database to connect to, this usually contained some information about the species of interest. This enabled for example the conversion of gene symbols to Ensembl gene IDs (since multiple species can have the same gene symbol). In remart, the mart argument is no longer required, and the species of interest is specified via the new species argument in getBM() and speciesL argument in getLDS().

New version argument

In biomaRt, the Ensembl version to query could be specified with the version argument (or directly in the host argument) in useEnsembl(). In remart, the version argument is now available in all functions that query Ensembl, and it is used to specify the Ensembl release to query. If not specified, the latest release will be used.