Abstract Research Objects have the potential to significantly enhance the reproducibility and transparency of scientific research. One important way Research Objects can do this is by encapsulating the means for re-executing the computational components of studies, thus supporting the new form of reproducibility enabled by digital computing---exact repeatability. However, Research Objects also can make scientific research more reproducible by supporting transparency, a component of reproducibility orthogonal to re-executability. We describe here our vision for making Research Objects more transparent by providing means for disambiguating claims about reproducibility generally, and computational repeatability specifically. We show how support for science-oriented queries can enable researchers to assess the reproducibility of Research Objects and the individual methods and results they encapsulate.