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