Computational Systems Biology Methods and Protocols.7z

Table 1(continued)Tool

Description

Requirements

Type

Interface

Operatingsystem

Programinglanguages References

NormalizationSingle-cell

normalization

A quantitative statistical method

to distinguish true biologicalvariability from the high levelsof technical noise in single-cellexperiments. This approachquantifies the statisticalsignificance of observed cell-to-cell variability in expressionstrength on a gene-by-genebasis

It is a complete workflow to

recreate all figures andnumbers shown in the paper.It is extensively commented inorder to demonstrate how oursuggested analysis method isperformed in practice andfacilitatere-implementation by the user

Package

Command

line

Unix/

Linux,Mac OS,Windows

R[

82

]

SAMstrt

The resampling-based bulk

normalization method inSAMseq is applied to spike-ins

Assumes that an equal number of

spike-in control RNAmolecules have been added toall samples

Package

Command

line

Unix/

Linux,Mac OS,Windows

R[

83

]

GRM

Fits polynomial gamma

regression model to FPKMdata from spike-ins; estimatedparameters are used to convertFPKM of endogenous genesto an absolute scale withineach cell

Performs within cell

normalization and may beused with FPKM, RPKM, orTPM

Package

Command

line

Unix/

Linux,Mac OS,Windows

R[

84

]

338 Yungang Xu and Xiaobo Zhou