Pseudotime Part 1: Monocle, Slingshot, Diffusion Pseudotime & Ordering Cells from a Snapshot

scRNA-seq captures one moment. Differentiation spans days. Pseudotime reconstructs the temporal order from a static snapshot.

Analogy: catching fish at random points along a river — ordering them by how far downstream they are.

- The snapshot problem — one time point, many developmental stages
- Pseudotime — biological progress, not clock time
- Monocle / Slingshot — principal graph fitting, branch point detection
- Diffusion pseudotime — Markov transitions from root (Board Game callback)
- Choosing the root — biology, velocity, or stemness

Foundation for: spatial transcriptomics pipeline (scVelo + CellRank), Census Bureau.

#Pseudotime #Monocle #Slingshot #DiffusionMap #scRNAseq #CellDifferentiation #Trajectory #Bioinformatics

Видео Pseudotime Part 1: Monocle, Slingshot, Diffusion Pseudotime & Ordering Cells from a Snapshot канала QSPplus

pseudotime analysis Monocle trajectory Slingshot lineage diffusion pseudotime principal graph cell differentiation ordering snapshot problem scRNA-seq branch point detection root cell selection developmental trajectory

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