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Table 1 Summary of existing lineage and pseudotime inference methods

From: Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

  Dimensionality reduction Cluster based Graph Pseudotime calculation Branching Supervision
Diffusion Pseudotime Diffusion maps No Weighted k-NN graph on cells Transition probabilities over arbitrary length random walks Yes Starting cell
Embeddr Laplacian eigenmaps No N/A Principal curve, orthogonal projection No Path direction1, subsetting2
Monocle ICA No MST on cells Diameter path, PQ trees Yes3 Path direction1, number of lineages
Monocle 2 Reversed graph embedding No Principal graph on cells Distance to root Yes Starting cluster
TSCAN PCA Yes MST on clusters Cluster centers, orthogonal projection Yes Starting cluster
Waterfall PCA Yes MST on clusters Cluster centers, orthogonal projection Yes4 Path direction1
Wishbone Diffusion maps No Ensemble of k-NN graphs on cells Distance refinement by waypoints Yes5 Starting cell
Slingshot Any Yes MST on clusters Simultaneous principal curves, orthogonal projection Yes Starting cluster, end clusters (optional)
  1. 1Some methods infer a single path or backbone and rely on the user to assign its directionality
  2. 2Methods that do not detect branching events require manually subsetting the data down to a single lineage
  3. 3Monocle does not detect the number of branching events, the number of lineages must be supplied by the user
  4. 4Waterfall detects branching events, but requires subsetting to a single lineage for pseudotime calculation
  5. 5Wishbone can only detect a single branching event (two lineages)