Single-Cell Trajectories Reconstruction, Exploration and Mapping of Omics Data with STREAM
ARTICLE https://doi.org/10.1038/s41467-019-09670-4 OPEN Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM Huidong Chen 1,2,3,4, Luca Albergante 5,6,7, Jonathan Y. Hsu1,8, Caleb A. Lareau 1,9, Giosuè Lo Bosco 10,11, Jihong Guan4, Shuigeng Zhou12, Alexander N. Gorban 13,14, Daniel E. Bauer9,15, Martin J. Aryee 1,3,9, David M. Langenau1,16, Andrei Zinovyev 5,6,7,14, Jason D. Buenrostro 9,17, Guo-Cheng Yuan 2,3,16 & Luca Pinello 1,9 1234567890():,; Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differ- entiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajec- tories 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. We have tested STREAM on several syn- thetic and real datasets generated with different single-cell technologies. We further demonstrate its utility for understanding myoblast differentiation and disentangling known heterogeneity in hematopoiesis for different organisms. STREAM is an open-source software package. 1 Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA. 2 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. 3 Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.
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