Computational Systems Biology Methods and Protocols.7z

Table 1(continued)Tool

Description

Requirements

Type

Interface

Operatingsystem

Programinglanguages References

Differential expression detectionSCDE

Models gene-specific expression

as a two-component mixture:a Poisson componentdescribes zero and a negativebinomial describes non-zeromeasurements

Requires un-normalized gene

expression counts (performsinternal correction) andprovides gene-specificposterior probabilities ofdifferential expression(DE) between two biologicalconditions. Tests for DE areperformed on non-zeros

Package

Command

line

Unix/

Linux,Mac OS,Windows

R[

88

]

powsimR

Simulates and evaluates

differential expression frombulk and especially single-cellRNA-seq data making itsuitable for a priori andposterior power analyses.Powsim is a flexible tool thatcan not only estimate samplesizes necessary to achieve acertain power but also informsabout the power to detectdifferential expression (DE) ina data set at hand. It can allowthe researcher to distinguishbetween actual discrepanciesand incongruities due to lackof power

NA

Package/

module

Command

line

Unix/

Linux,Mac OS,Windows

R[

89

]

340 Yungang Xu and Xiaobo Zhou