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Single-cell proteomic datasets can be acquired using various modalities, including CyTOF, CITE-seq and CODEX, on different biological samples or species (for example, human or NHP) with shared underlying biological information. Protein markers are divided into two classes: (1) features captured within both datasets (shared features), and (2) markers not shared between the datasets (distinct features). Both classes of protein expression matrices serve as inputs to the MARIO algorithm.

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