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RESEARCH PRODUCT
Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM
Luca PinelloLuca PinelloGengyang YuanLuca AlberganteLuca AlberganteJonathan Y. HsuJonathan Y. HsuJason D. BuenrostroJason D. BuenrostroDavid M. LangenauCaleb A. LareauCaleb A. LareauShuigeng ZhouAndrei ZinovyevMartin J. AryeeMartin J. AryeeHuidong ChenAlexander N. GorbanDaniel E. BauerDaniel E. BauerJihong GuanGiosuè Lo Boscosubject
0301 basic medicineEpigenomicsMultifactor Dimensionality ReductionComputer scienceGeneral Physics and Astronomy02 engineering and technologyOmics dataMyoblastsMiceSingle-cell analysisGATA1 Transcription FactorMyeloid CellsLymphocyteslcsh:ScienceData processingMultidisciplinaryQGene Expression Regulation DevelopmentalRNA sequencingCell DifferentiationGenomics021001 nanoscience & nanotechnologyData processingDNA-Binding ProteinsInterferon Regulatory FactorsSingle-Cell Analysis0210 nano-technologyAlgorithmsOmics technologiesSignal TransductionLineage differentiationScienceComputational biologyGeneral Biochemistry Genetics and Molecular BiologyArticle03 medical and health sciencesErythroid CellsAnimalsCell LineageGeneral Chemistrydevelopmental trajectories visualizationHematopoietic Stem CellsPipeline (software)Visualization030104 developmental biologyTheoryofComputation_MATHEMATICALLOGICANDFORMALLANGUAGESCellular heterogeneitySingle cell analysilcsh:QGene expressionTranscriptomeTranscription Factorsdescription
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.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2019-04-01 | Nature Communications |