Computational Systems Biology Methods and Protocols.7z

Embeddr

Laplacian Eigenmaps and

principal curves forpseudotemporal ordering andclustering of single-cellRNA-seq data. Embeddrcreates a reduced dimensionalrepresentation of the genespace using a high-variancegene correlation graph andLaplacian Eigenmaps. It thenfits a smooth pseudotimetrajectory using principalcurves

NA

Package

Command

line

Unix/

Linux,Mac OS,Windows

R[

113

]

Dimensionality reductionZIFA

Models dropout rate as a

function of expression in afactor analysis (lineardimension reduction)framework

Requires normalized,

log-transformed estimates ofgene expression (zeros are nottransformed)

Package

Command

line

Unix/

Linux

Python

[^98

]

ZINB-WaVE ZINB-WaVE is a general and

flexible zero-inflated negativebinomial model which is ableto give a more stable andaccurate low dimensionalrepresentation of the data thanprincipal component analysis(PCA) and zero-inflated factoranalysis (ZIFA), without theneed for a preliminarynormalization step

NA

Package

Command

line

Unix/

Linux,Mac OS,Windows

R[

114

]

(continued)

Applications of Single-Cell Sequencing for Multiomics 349