Cannoodt, RobrechtSaelens, WouterDeconinck, LouiseSaeys, Yvan2021-07-172021-07-172021-07-172021-06-2410.1038/s41467-021-24152-2https://infoscience.epfl.ch/handle/20.500.14299/180037WOS:000669489100005We present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimulating development and testing of computational methods. We demonstrate its potential for spearheading computational methods on three applications: aligning cell developmental trajectories, cell-specific regulatory network inference and estimation of RNA velocity. To benchmark single cell bioinformatics tools, data simulators can provide a robust ground truth. Here the authors present dyngen, a multi-modal simulator, and apply it to aligning cell developmental trajectories, cell-specific regulatory network inference and estimation of RNA velocity.Multidisciplinary SciencesScience & Technology - Other Topicsnetwork inferencegene-expressiontranscriptiontrajectoriesantagonismgenerationtext::journal::journal article::research article