Table 1(continued)Tool
Description
Requirements
Type
Interface
Operatingsystem
Programinglanguages References
proportion of cells withinmodes (DP), differ in thenumber of modes (DM), orare both DE and DM (DB)
TASC
Incorporates the technical
parameters, which reflect cell-to-cell batch effects, into ahierarchical mixture model toestimate the biologicalvariance of a gene and detectdifferentially expressed genes.TASC is a statisticalframework, to reliably modelthe cell-specific dropout ratesand amplification bias by useof external RNA spike-ins. It isprogrammed to becomputationally efficient,taking advantage of multi-threaded parallelization
Boost C++ Library, GNU
Scientific Library, cmake, gcc
Framework Command
line
Unix/
Linux,Mac OS,Windows
C[
94
]
SpatialDE
Identifies and characterizes
spatially variable genes.SpatialDE is based onGaussian process regression(GPR) that decomposes theexpression variability into aspatial and non-spatialcomponent. It can be used totest for spatial expressionvariation in cell culturesystems, where spatialvariation may not be expecteda priori
The tool is useful in expression
data type with spatial and/ortemporal resolution
Package/
Module
Command
line
Unix/
Linux
Python
[^95
]
342 Yungang Xu and Xiaobo Zhou