Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

Huidong Chen, Luca Albergante, Jonathan Y. Hsu, Caleb A. Lareau, Giosuè Lo Bosco, Jihong Guan, Shuigeng Zhou, Alexander N. Gorban, Daniel E. Bauer, Martin J. Aryee, David M. Langenau, Andrei Zinovyev, Jason D. Buenrostro, Guo-Cheng Yuan () and Luca Pinello ()
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Huidong Chen: Massachusetts General Hospital Research Institute and Harvard Medical School
Luca Albergante: PSL Research University
Jonathan Y. Hsu: Massachusetts General Hospital Research Institute and Harvard Medical School
Caleb A. Lareau: Massachusetts General Hospital Research Institute and Harvard Medical School
Giosuè Lo Bosco: University of Palermo
Jihong Guan: Tongji University
Shuigeng Zhou: Fudan University
Alexander N. Gorban: University of Leicester
Daniel E. Bauer: Broad Institute of MIT and Harvard
Martin J. Aryee: Massachusetts General Hospital Research Institute and Harvard Medical School
David M. Langenau: Massachusetts General Hospital Research Institute and Harvard Medical School
Andrei Zinovyev: PSL Research University
Jason D. Buenrostro: Broad Institute of MIT and Harvard
Guo-Cheng Yuan: Dana-Farber Cancer Institute
Luca Pinello: Massachusetts General Hospital Research Institute and Harvard Medical School

Nature Communications, 2019, vol. 10, issue 1, 1-14

Abstract: Abstract 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. We have tested STREAM on several synthetic 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.

Date: 2019
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DOI: 10.1038/s41467-019-09670-4

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