单细胞-拟时间分析

单细胞轨迹推断/拟时间分析

• cell cycle
• cell differentiatioon
• cell activation

前提假设：细胞相同的表达量，来自同一个lineage

拟时间分析方法

• Dimensional reduction
  • MST (Monocle)
  • Smooth curve (Slingshot)
• Nearest Neighbor Graph-Based Algorithms(Wishbone, shortest walks)
• Cluster networks (StemID, cluster centers)
• Spliced and unspliced mRNA: (RNA velocity: the direction and the speed of differentiation)

参考

• Single-cell RNA-seq pseudotime estimation algorithms
• 用于单细胞数据分析的软件包列表
• Benchmarking trajectory inference methods
• Single-Cell Transcriptomics Meets Lineage Tracing
• A comparison of single-cell trajectory inference methods