# Simple Simulation of Single-cell RNA Sequencing Data

## Documentation for package ‘splatter’ version 1.2.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G L M N P R S W Z

splatter-package | splatter.

## -- A --

addFeatureStats | Add feature statistics
addGeneLengths | Add gene lengths

## -- B --

BASiCSEstimate | Estimate BASiCS simulation parameters
BASiCSEstimate.matrix | Estimate BASiCS simulation parameters
BASiCSEstimate.SCESet | Estimate BASiCS simulation parameters
BASiCSParams | The BASiCSParams class
BASiCSParams-class | The BASiCSParams class
BASiCSSimulate | BASiCS simulation
bridge | Brownian bridge

## -- C --

compareSCEs | Compare SingleCellExperiment objects

## -- D --

diffSCEs | Diff SingleCellExperiment objects

## -- E --

expandParams | Expand parameters
expandParams-method | Expand parameters

## -- G --

getLNormFactors | Get log-normal factors
getParam | Get a parameter
getParam-method | Get a parameter
getParams | Get parameters
getPathOrder | Get path order

## -- L --

listSims | List simulations
logistic | Logistic function
lun2Estimate | Estimate Lun2 simulation parameters
lun2Estimate.matrix | Estimate Lun2 simulation parameters
lun2Estimate.SingleCellExperiment | Estimate Lun2 simulation parameters
Lun2Params | The Lun2Params class
Lun2Params-class | The Lun2Params class
lun2Simulate | Lun2 simulation
lunEstimate | Estimate Lun simulation parameters
lunEstimate.matrix | Estimate Lun simulation parameters
lunEstimate.SingleCellExperiment | Estimate Lun simulation parameters
LunParams | The LunParams class
LunParams-class | The LunParams class
lunSimulate | Lun simulation

## -- M --

makeCompPanel | Make comparison panel
makeDiffPanel | Make difference panel
makeOverallPanel | Make overall panel
mfaEstimate | Estimate mfa simulation parameters
mfaEstimate.matrix | Estimate mfa simulation parameters
mfaEstimate.SingleCellExperiment | Estimate mfa simulation parameters
MFAParams | The MFAParams class
MFAParams-class | The MFAParams class
mfaSimulate | MFA simulation

## -- N --

newBASiCSParams | New Params
newLun2Params | New Params
newLunParams | New Params
newMFAParams | New Params
newParams | New Params
newPhenoParams | New Params
newSCDDParams | New Params
newSimpleParams | New Params
newSplatParams | New Params
newZINBParams | New Params

## -- P --

Params | The Params virtual class
Params-class | The Params virtual class
phenoEstimate | Estimate PhenoPath simulation parameters
phenoEstimate.matrix | Estimate PhenoPath simulation parameters
phenoEstimate.SingleCellExperiment | Estimate PhenoPath simulation parameters
PhenoParams | The PhenoParams class
PhenoParams-class | The PhenoParams class
phenoSimulate | PhenoPath simulation

## -- R --

rbindMatched | Bind rows (matched)

## -- S --

scDDEstimate | Estimate scDD simulation parameters
scDDEstimate.default | Estimate scDD simulation parameters
scDDEstimate.matrix | Estimate scDD simulation parameters
scDDEstimate.SingleCellExperiment | Estimate scDD simulation parameters
SCDDParams | The SCDDParams class
SCDDParams-class | The SCDDParams class
scDDSimulate | scDD simulation
setParam | Set a parameter
setParam-method | Set a parameter
setParams | Set parameters
setParamsUnchecked | Set parameters UNCHECKED
setParamUnchecked | Set a parameter UNCHECKED
setParamUnchecked-method | Set a parameter UNCHECKED
showPP | Show pretty print
simpleEstimate | Estimate simple simulation parameters
simpleEstimate.matrix | Estimate simple simulation parameters
simpleEstimate.SingleCellExperiment | Estimate simple simulation parameters
SimpleParams | The SimpleParams class
SimpleParams-class | The SimpleParams class
simpleSimulate | Simple simulation
splatEstBCV | Estimate Splat Biological Coefficient of Variation parameters
splatEstDropout | Estimate Splat dropout parameters
splatEstimate | Estimate Splat simulation parameters
splatEstimate.matrix | Estimate Splat simulation parameters
splatEstimate.SingleCellExperiment | Estimate Splat simulation parameters
splatEstLib | Estimate Splat library size parameters
splatEstMean | Estimate Splat mean parameters
splatEstOutlier | Estimate Splat expression outlier parameters
SplatParams | The SplatParams class
SplatParams-class | The SplatParams class
splatSimBatchCellMeans | Simulate batch means
splatSimBatchEffects | Simulate batch effects
splatSimBCVMeans | Simulate BCV means
splatSimCellMeans | Simulate cell means
splatSimDE | Simulate group differential expression
splatSimDropout | Simulate dropout
splatSimGeneMeans | Simulate gene means
splatSimGroupCellMeans | Simulate cell means
splatSimGroupDE | Simulate group differential expression
splatSimLibSizes | Simulate library sizes
splatSimPathCellMeans | Simulate cell means
splatSimPathDE | Simulate group differential expression
splatSimSingleCellMeans | Simulate cell means
splatSimTrueCounts | Simulate true counts
splatSimulate | Splat simulation
splatSimulateGroups | Splat simulation
splatSimulatePaths | Splat simulation
splatSimulateSingle | Splat simulation
splatter | splatter.
summariseDiff | Summarise diffSCESs

## -- W --

winsorize | Winsorize vector

## -- Z --

zinbEstimate | Estimate ZINB-WaVE simulation parameters
zinbEstimate.matrix | Estimate ZINB-WaVE simulation parameters
zinbEstimate.SingleCellExperiment | Estimate ZINB-WaVE simulation parameters
ZINBParams | The ZINBParams class
ZINBParams-class | The ZINBParams class
zinbSimulate | ZINB-WaVE simulation