switchde: inference of switch-like differential expression along single-cell trajectories.
switchde: inference of switch-like differential expression along single-cell trajectories.
复制标题
DOI：
10.1093/bioinformatics/btw798
复制
发表时间：
2017-04-15
期刊：
影响因子：
--
通讯作者：
Yau C
中科院分区：
文献类型：
--
作者：
Campbell KR;Yau C
单细胞RNA序列数据的伪时间分析已经变得越来越普遍。通常，与感兴趣的生物过程相对应的潜在轨迹--例如分化或细胞周期--被发现。然而，对沿着这样的轨迹建立基因差异表达模型的关注相对较少。我们提出了Switchde，一个统计框架和伴随的R包，用于识别沿着伪时间轨迹的基因的开关样差异表达。我们的方法包括快速模型拟合，它提供对应于基因上调或下调的速度以及这种调控发生在轨迹中的位置的可解释的参数估计。它还报告了一个P值，支持拒绝常量表达式模型来进行开关式差分表达式，并可选地对单元格数据中普遍存在的零膨胀进行建模。R Package Switchde可通过https://bioconductor.org/packages/switchde.的BioConductor项目获得补充数据可在生物信息学在线上获得。
Pseudotime analyses of single-cell RNA-seq data have become increasingly common. Typically, a latent trajectory corresponding to a biological process of interest—such as differentiation or cell cycle—is discovered. However, relatively little attention has been paid to modelling the differential expression of genes along such trajectories. We present switchde, a statistical framework and accompanying R package for identifying switch-like differential expression of genes along pseudotemporal trajectories. Our method includes fast model fitting that provides interpretable parameter estimates corresponding to how quickly a gene is up or down regulated as well as where in the trajectory such regulation occurs. It also reports a P-value in favour of rejecting a constant-expression model for switch-like differential expression and optionally models the zero-inflation prevalent in single-cell data. The R package switchde is available through the Bioconductor project at https://bioconductor.org/packages/switchde. Supplementary data are available at Bioinformatics online.