Table 2 Comparison of trajectory inference methods using scRNA-seq

From: Single-cell RNA sequencing technologies and bioinformatics pipelines

Methods Dimensionality reduction Main strategy Required input Environment
SCUBA pseudotime t-SNE Principal curve None Matlab
Monocle ICA and MST Differential expression Time points R (Bioconductor)
Waterfall PCA, K-means and MST Clustering cells None R
Wishbone PCA, Diffusion maps, Boostrap k-NNG Ensemble Starting cell Python
  1. scRNA single-cell RNA sequencing, SCUBA single-cell clustering using bifurcation analysis, t-SNE t-distributed stochastic neighbor embedding, ICA independent component analysis, MST minimum spanning tree, PCA principal component analysis, k-NNG k-nearest neighbor graph