单细胞轨迹推断/拟时间分析 Trajectory inference/pseudotime analysis

• Trajectory inference:轨迹推断
• pseudotime analysis: 拟时间分析

研究的对象

• cell cycle：G1、S、G2、M之间的变换
• 细胞分化：发育中的干细胞、祖细胞分化出特定的细胞类型
• 研究细胞状态的转化，静息->激活

^{saelensComparisonSinglecellTrajectory2019}

https://github.com/dynverse/dynbenchmark

资源

• Single-cell RNA-seq pseudotime estimation algorithms

• List of software packages (and the people developing these methods) for single-cell data analysis

• Monocle is a toolkit for analyzing single-cell gene expression experiments. Monocle was designed for RNA-Seq, but can also work with single cell qPCR. It performs differential expression analysis, and can find genes that differ between cell types or between cell states. When used to study an ongoing biological process such as cell differentiation, Monocle learns that process and places cells in order according to their progress through it. Monocle finds genes that are dynamically regulated during that process.

• Monocle: Differential expression for single-cell RNA-Seq and qPCR.