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SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development

By Robrecht Cannoodt, Wouter Saelens, Dorine Sichien, Simon Tavernier, Sophie Janssens, Martin Guilliams, Bart Lambrecht, Katleen De Preter, Yvan Saeys

Posted 06 Oct 2016
bioRxiv DOI: 10.1101/079509

Recent advances in RNA sequencing enable the generation of genome-wide expression data at the single-cell level, opening up new avenues for transcriptomics and systems biology. A new application of single-cell whole-transcriptomics is the unbiased ordering of cells according to their progression along a dynamic process of interest. We introduce SCORPIUS, a method which can effectively reconstruct an ordering of individual cells without any prior information about the dynamic process. Comprehensive evaluation using ten scRNA-seq datasets shows that SCORPIUS consistently outperforms state-of-the-art techniques. We used SCORPIUS to generate novel hypotheses regarding dendritic cell development, which were subsequently validated in vivo. This work enables data-driven investigation and characterization of dynamic processes and lays the foundation for objective benchmarking of future trajectory inference methods.

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