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Table 1 Input parameters for the Splat simulation model

From: Splatter: simulation of single-cell RNA sequencing data

Name

Symbol

Description

Mean shape

\( \upalpha \)

Shape parameter for the mean gene expression gamma distribution

Mean rate

\( \upbeta \)

Rate parameter for the mean gene expression gamma distribution

Library size location

\( {\upmu}^{\mathrm{L}} \)

Location parameter for the library size log-normal distribution

Library size scale

\( {\upsigma}^{\mathrm{L}} \)

Scale parameter for the library size log-normal distribution

Outlier probability

\( {\uppi}^{\mathrm{O}} \)

Probability that a gene is an expression outlier

Outlier location

\( {\upmu}^{\mathrm{O}} \)

Location parameter for the expression outlier factor log-normal distribution

Outlier scale

\( {\upsigma}^{\mathrm{O}} \)

Scale parameter for the expression outlier factor log-normal distribution

Common BCV

\( \upphi \)

Common BCV dispersion across all genes

BCV degrees of freedom

\( \mathrm{df} \)

Degrees of freedom for the BCV inverse chi-squared distribution

Dropout midpoint

\( {\mathrm{x}}_0 \)

Midpoint for the dropout logistic function

Dropout shape

\( \mathrm{k} \)

Shape of the dropout logistic function