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MotivationWe are witnessing an enormous growth in the amount of molecular profiling (-omics) data. The integration of multi-omics data is challenging. Moreover, human multi-omics data may be privacy-sensitive and misused to de-anonymize and (re-)identify individuals. Hence, most data is kept in secure and protected silos. Therefore, it remains a challenge to reuse these data without infringing the privacy of the individuals from which the data were derived. Federated analysis of FAIR data is a privacy-preserving solution to make optimal use of these multi-omics data and transform them into actionable knowledge.ResultsThe Netherlands X-omics Initiative is a National Roadmap Large-Scale Research Infrastructure aiming for efficient integration of data generated within X-omics and external datasets. To facilitate this, we developed the FAIR Data Cube (FDCube), which adopts and applies the FAIR principles and helps researchers to create FAIR data and metadata, facilitate reuse of their data, and make their data analysis workflows transparent. The FDCube also meets security-by-design and privacy-by-design principles.Availabilityhttps://github.com/Xomics/FAIRDataCubeContactXiaofeng.Liao@radboudumc.nl,Peter-Bram.tHoen@radboudumc.nlSupplementary informationSupplementary data are available atBioinformaticsonline.