Computational Systems Biology Methods and Protocols.7z

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[

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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

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342 Yungang Xu and Xiaobo Zhou