Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM
Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM
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使用 STREAM 组学数据的单细胞轨迹重建、探索和绘图
DOI：
10.1038/s41467-019-09670-4
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发表时间：
2019-04-23
影响因子：
16.6
通讯作者：
Pinello, Luca
中科院分区：
文献类型：
--
作者：
Chen, Huidong;Albergante, Luca;Pinello, Luca
单细胞转录组学分析已经使得谱系分化轨迹的从头重建成为可能，沿着细胞异质性和状态转换的表征。已经开发了几种方法来从单细胞转录组数据重建发育轨迹，但在分析单细胞表观基因组数据和轨迹可视化方面的努力仍然有限。在这里，我们提出了STREAM，一个交互式管道，能够从单细胞转录组和表观基因组数据中解开和可视化复杂的分支轨迹。我们已经在几个合成和真实的数据集上测试了STREAM，这些数据集是用不同的单细胞技术生成的。我们进一步证明了它的效用，了解成肌细胞分化和解开已知的异质性造血不同的生物体。STREAM是一个开源软件包。
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.