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
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