Computational Systems Biology Methods and Protocols.7z

identifying genes that aredifferentially expressedbetween time points or, if dataat multiple time points are notavailable, choosing genesabove a mean and variancethreshold

Oscope

Uses a paired-sine model and

K-medoids clustering toidentify groups of oscillatorygenes. For each oscillatorygroup, an extended nearestinsertion algorithm is used toconstruct the cyclic order ofcells, defined as the order thatspecifies each cell’s positionwithin one cycle of theoscillation of that group

Identifies groups of oscillatory

genes, when present. Requiresnormalized gene expressionand use of only high mean,high-variance genes isrecommended

Package

Command

line

Unix/

Linux,Mac OS,Windows

R[

102

]

TSCAN

A software tool developed to

better support in silicopseudotime reconstruction insingle-cell RNA-seq analysis.TSCAN uses a cluster-basedminimum spanning tree(MST) approach to order cells.TSCAN has a graphical userinterface (GUI) to supportdata visualization and userinteraction

Single-cell data should be

prepared in a matrix-like dataformat. Each row correspondsto a gene/feature and eachcolumn corresponds to asingle cell

Package

Command

line/Webuserinterface

Unix/

Linux,Mac OS,Windows

R[

103

]

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Applications of Single-Cell Sequencing for Multiomics 345