Computational Systems Biology Methods and Protocols.7z

Table 1(continued)Tool

Description

Requirements

Type

Interface

Operatingsystem

Programinglanguages References

Destiny

Extends diffusion maps

(a nonlinear dimensionreduction approach) to handlezeros and sampling densityheterogeneities inherent insingle-cell data

Requires variance-stabilized

gene expression estimates;works best with a largenumber of cells

Package

Command

line

Unix/

Linux,Mac OS,Windows

R[

99

]

SNN-Cliq

Clusters cells by identifying and

merging subgraphs (quasi-cliques) in a shared nearestneighbor (SNN) graph; thenumber of clusters is chosenautomatically

Requires a reduced set of genes.

The authors recommendusing genes with averageRPKM

>

20 and using a log

transformation to reduce theeffect of outliers. Relies on avalid choice of graphparameters

Package

Command

line

Unix/

Linux

MATLAB,

Python

[^100

]

SCUBA

Uses k-means to cluster data

along a binary tree detailingbifurcation events for timecourse data. Modelsexpression regulation alongthe tree using bifurcationtheory

Requires a reduced set of genes.

The authors recommendusing the 1000 most variablegenes that are expressed in atleast 30% of cells

Package

Command

line

Unix/

Linux,Mac OS,Windows

MATLAB [

101

]

Cell lineage and pseudotime inferenceMonocle

Reduces data using independent

component analysis (ICA) andconstructs a minimumspanning tree (MST) to ordercells in pseudotime

Requires normalized,

log-transformed geneexpression estimates and areduced set of genes. Theauthors recommend

Toolkit

Command

line

Unix/

Linux,Mac OS

[^30

]

344 Yungang Xu and Xiaobo Zhou