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Understanding the flow of deformable particles such as liquid drops, synthetic capsules and vesicles, and biological cells confined in a small channel is essential to a wide range of potential chemical and biomedical engineering applications. Computer simulations of this kind of fluid-structure (membrane) interaction in low-Reynolds-number flows raise significant challenges faced by an intricate interplay between flow stresses, complex particles' interfacial mechanical properties, and fluidic confinement. Here, we present an isogeometric computational framework by combining the finite-element method (FEM) and boundary-element method (BEM) for an accurate prediction of the deformation and motion of a single soft particle transported in microfluidic channels. The proposed numerical framework is constructed consistently with the isogeometric analysis paradigm; Loop's subdivision elements are used not only for the representation of geometry but also for the membrane mechanics solver (FEM) and the interfacial fluid dynamics solver (BEM). We validate our approach by comparison of the simulation results with highly accurate benchmark solutions to two well-known examples available in the literature, namely a liquid drop with constant surface tension in a circular tube and a capsule with a very thin hyperelastic membrane in a square channel. We show that the numerical method exhibits second-order convergence in both time and space. To further demonstrate the accuracy and long-time numerically stable simulations of the algorithm, we perform hydrodynamic computations of a lipid vesicle with bending stiffness and a red blood cell with a composite membrane in capillaries. The present work offers some possibilities to study the deformation behavior of confining soft particles, especially the particles' shape transition and dynamics and their rheological signature in channel flows.