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STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

By Huidong Chen, Luca Albergante, Jonathan Y Hsu, Caleb Lareau, Giosuè Lo Bosco, Jihong Guan, Shuigeng Zhou, Alexander N. Gorban, Daniel E. Bauer, Martin Aryee, David M. Langenau, A Zinovyev, Jason Daniel Buenrostro, Guo-Cheng Yuan, Luca Pinello

Posted 18 Apr 2018
bioRxiv DOI: 10.1101/302554 (published DOI: 10.1038/s41467-019-09670-4)

Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data.

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