Journal
NATURE COMMUNICATIONS
Volume 10, Issue -, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41467-019-09670-4
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Funding
- Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation [2018-182734]
- National Human Genome Research Institute (NHGRI) Career Development Award [R00HG008399]
- Claudia Adams Barr Award
- Bridge Award
- Harvard Society of Fellows
- Allen Distinguished Investigator Program, through The Paul G. Allen Frontiers Group
- ITMO Cancer SysBio program (MOSAIC)
- INCa PLBIO program (CALYS) [INCA_11692]
- NHLBI [DP2OD022716, P01HL032262]
- Burroughs Wellcome Fund
- Ministry of Education and Science of Russia [14.Y26.31.0022]
- National Natural Science Foundation of China (NSFC) [61772367]
- National Key Research and Development Program of China [2016YFC0901704]
- Broad Institute Fellowship
- [R24OD016761]
- [R01CA211734]
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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.
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