Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.
Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.
复制标题
弹弓：单细胞转录组学的细胞谱系和伪时间推断。
DOI：
10.1186/s12864-018-4772-0
复制
发表时间：
2018-06-19
期刊：
影响因子：
4.4
通讯作者：
Dudoit S
中科院分区：
文献类型：
--
作者：
Street K;Risso D;Fletcher RB;Das D;Ngai J;Yosef N;Purdom E;Dudoit S
单细胞转录学使研究人员能够研究复杂的异质细胞群落。它可以应用于干细胞及其后代，以便绘制从多能祖细胞到完全分化细胞的过程。虽然已经提出了各种统计和计算方法来推断细胞谱系，但准确描述多个分支谱系的问题仍然难以解决。我们介绍了Slingshot，一种从单细胞基因表达数据中推断细胞谱系和假时间的新方法。在以前发表的数据集中，Slingshot正确地识别了一到三个分支轨迹的生物信号。此外，我们的模拟研究表明，Slingshot方法比其他领先的方法推断出更准确的伪时间。弹弓是一种独特的坚固而灵活的工具，它结合了噪声单一单元数据所需的高度稳定的技术与识别多个轨迹的能力。准确的谱系推断是鉴定动态时间基因表达的关键步骤。本文的在线版本(10.1186/s12864-0184772-0)包含补充材料，可供授权用户使用。
Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve. We introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods. Slingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression. The online version of this article (10.1186/s12864-018-4772-0) contains supplementary material, which is available to authorized users.