Computational Systems Biology Methods and Protocols.7z

SCnorm

A quantile regression method for

accurate and efficientnormalization of scRNA-seqdata. SCnorm uses quantileregression to estimate thedependence of read counts onsequencing depth for everygene. Genes with similardependence are then grouped,and a second quantileregression is used to estimatescale factors within each group

SCnorm does not require spike-

ins, and performance may beimproved if good spike-ins areavailable

Package

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line

Unix/

Linux,Mac OS,Windows

R[

85

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NODES

A normalization technique that

substantially reduces technicalvariability and improves thequality of downstreamanalyses. NODES provides atransformative reduction incomputational complexity andexecution time, which will becrucial for analyzing themassive single-cell data setsgenerated by inDrop/Drop-seq and other high-throughput single-celltechnologies

NA

Package

Command

line

Unix/

Linux,Mac OS,Windows

R[

86

]

SCONE

An R package for single-cell

RNA-seq data quality controland normalization. This data-driven framework usessummaries of expression datato assess the efficacy ofnormalization workflows

R (R version 3.3)

Package

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line

Unix/

Linux,Mac OS,Windows

R[

87

]

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Applications of Single-Cell Sequencing for Multiomics 339