# Simple Simulation of Single-cell RNA Sequencing Data

## Documentation for package ‘splatter’ version 1.18.2

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

## Help Pages

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

## -- A --

addFeatureStats | Add feature statistics
addGeneLengths | Add gene lengths

## -- B --

BASiCSEstimate | Estimate BASiCS simulation parameters
BASiCSEstimate.matrix | Estimate BASiCS simulation parameters
BASiCSEstimate.SingleCellExperiment | Estimate BASiCS simulation parameters
BASiCSParams | The BASiCSParams class
BASiCSParams-class | The BASiCSParams class
BASiCSSimulate | BASiCS simulation
bridge | Brownian bridge
bringItemsForward | Bring items forward

## -- C --

checkDependencies | Check dependencies
co.var | Calculate coefficient of variation
compareSCEs | Compare SingleCellExperiment objects

## -- D --

diffSCEs | Diff SingleCellExperiment objects

## -- E --

expandParams | Expand parameters
expandParams-method | Expand parameters

## -- G --

getBetaStepProbs | Get Beta step probabilities
getCounts | Get counts
getLNormFactors | Get log-normal factors
getParam | Get a parameter
getParam-method | Get a parameter
getParams | Get parameters
getPathOrder | Get path order

## -- K --

kersplatEstBCV | Estimate Kersplat BCV parameters
kersplatEstimate | Estimate Kersplat simulation parameters
kersplatEstimate.matrix | Estimate Kersplat simulation parameters
kersplatEstimate.SingleCellExperiment | Estimate Kersplat simulation parameters
kersplatEstLib | Estimate Kersplat library size parameters
kersplatEstMean | Estimate Kersplat means
kersplatGenNetwork | Generate Kersplat gene network
KersplatParams | The KersplatParams class
KersplatParams-class | The KersplatParams class
kersplatSample | Kersplat sample
kersplatSelectRegs | Select Kersplat regulators
kersplatSetup | Kersplat setup
kersplatSimAmbientCounts | Simulate Kersplat ambient counts
kersplatSimCellCounts | Simulate Kersplat cell counts
kersplatSimCellMeans | Simulate Kersplat cell means
kersplatSimCounts | Simulate Kersplat final counts
kersplatSimGeneMeans | Simulate Kersplat gene means
kersplatSimLibSizes | Simulate Kersplat library sizes
kersplatSimPaths | Simulate Kersplat paths
kersplatSimulate | Kersplat simulation

## -- 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
minimiseSCE | Minimise SCE
mockBulkeQTL | Generate mock eQTL mapping results
mockBulkMatrix | Generate mock bulk population scale expression data
mockEmpiricalSet | Generate set of "empirical" mock data
mockGFF | Generate mock gff
mockVCF | Generate mock vcf

## -- N --

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

## -- P --

Params | The Params virtual class
Params-class | The Params virtual class
paramsExpander | Expand parameters
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 --

sampleDensity | Sample density
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
selectFit | Select fit
setParam | Set a parameter
setParam-method | Set a parameter
setParams | Set parameters
setParams-method | Set parameters
setParamsUnchecked | Set parameters UNCHECKED
setParamUnchecked | Set a parameter UNCHECKED
setParamUnchecked-method | Set a parameter UNCHECKED
showDFs | Show data.frame
showPP | Show pretty print
showValues | Show values
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
sparseDCEstimate | Estimate SparseDC simulation parameters
sparseDCEstimate.matrix | Estimate SparseDC simulation parameters
sparseDCEstimate.SingleCellExperiment | Estimate SparseDC simulation parameters
SparseDCParams | The SparseDCParams class
SparseDCParams-class | The SparseDCParams class
sparseDCSimulate | SparseDC simulation
sparsifyMatrices | Sparsify matrices
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
splatPopAssignMeans | Sample expression mean and variance for each gene
splatPopCleanSCE | Clean up the population-scale SCE to remove redundant information
splatPopConditionalEffects | Add conditional DE effects to means matrix
splatPopConditionEffects | Assign Condition-specific eQTL and DEGs.
splatPopDesignBatches | Set up pooled experimental design
splatPopDesignConditions | Set up designed experiments conditions
splatPopeQTLEffects | Assign eGenes-eSNPs pairs and effect sizes.
splatPopEstimate | Estimate population/eQTL simulation parameters
splatPopEstimateEffectSize | Estimate eQTL Effect Size parameters
splatPopEstimateMeanCV | Estimate gene mean and gene mean variance parameters
splatPopGroupEffects | Assign group-specific eQTL and DEGs.
SplatPopParams | The SplatPopParams class
SplatPopParams-class | The SplatPopParams class
splatPopParseEmpirical | splatPopParseEmpirical
splatPopParseGenes | Generate population key matrix from random or gff provided gene information
splatPopParseVCF | Format and subset genotype data from a VCF file.
splatPopQuantNorm | Quantile normalize by sample to fit sc expression distribution.
splatPopQuantNormKey | Add quantile normalized gene mean and cv info the eQTL key.
splatPopSimBatchEffects | Simulate batch effects
splatPopSimConditionalEffects | Add conditional DE effects to means matrix
splatPopSimEffects | Add eQTL effects to means matrix
splatPopSimGeneMeans | Simulate gene means for splatPop
splatPopSimMeans | Simulate mean gene expression matrix without eQTL effects
splatPopSimulate | splatPop simulation
splatPopSimulateMeans | splatPopSimulateMeans
splatPopSimulateSample | splatPopSimulateSample simulation
splatPopSimulateSC | splatPopSimulateSC
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 diffSCEs
summariseKS | Summarise KS
summariseStats | Summarise statistics

## -- T --

tidyStatSumm | Tidy summarised statistics

## -- 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