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Combinatorial CRISPR screens are a well-established tool for the investigation of genetic interactions in a high-throughput fashion. Currently advancements from 2D combinatorial CRISPR screens towards 3D combinatorial screens are made, but at the same time an easy-to-use computational method for the analysis of 3D combinatorial screens is missing. Here we propose a Bayesian analysis method for 3D CRISPR screens based on a well-established 2D CRISPR screen analysis protocol. Hoping to provide researchers with an out-of-the-box analysis solution, avoiding the need for time and resource intensive development of custom analysis protocols.